From 6f5c6b26f64d37512fe867e7840a1f65dd545eae Mon Sep 17 00:00:00 2001 From: Hannah-Doerpholz <108814050+Hannah-Doerpholz@users.noreply.github.com> Date: Thu, 5 Sep 2024 10:03:27 +0200 Subject: [PATCH] Update DPBO.owl testing the workflow --- DPBO.owl | 9456 ++++++++++++++++++++++++++++-------------------------- 1 file changed, 4881 insertions(+), 4575 deletions(-) diff --git a/DPBO.owl b/DPBO.owl index 5785c49..7acf131 100644 --- a/DPBO.owl +++ b/DPBO.owl @@ -1,34 +1,34 @@ - - - - https://orcid.org/0000-0001-9021-3197 - https://orcid.org/0000-0003-1476-2121 - DataPLANT Biology Ontology - DPBO - 1.2 - muehlhaus - MIAPPE - NCBITaxon - NCIT - NFDI4PSO - coverage: Missing Terms for the DataPLANT end-point repository templates - creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de> - creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de> - curator: Kathryn Dumschott <k.dumschott@fz-juelich.de> - curator: Stella Eggels <s.eggels@fz-juelich.de> + + + https://orcid.org/0000-0001-9021-3197 + https://orcid.org/0000-0003-1476-2121 + DataPLANT Biology Ontology + DPBO + 1.2 + muehlhaus + MIAPPE + NCBITaxon + NCIT + NFDI4PSO + coverage: Missing Terms for the DataPLANT end-point repository templates + creator: Dominik Brilhaus <dominik.brilhaus<-at->hhu.de> + creator: Hajira Jabeen <hajira.jabeen<-at->uni-koeln.de> + curator: Kathryn Dumschott <k.dumschott@fz-juelich.de> + curator: Stella Eggels <s.eggels@fz-juelich.de> @@ -71,7 +71,7 @@ - definition + definition @@ -106,33 +106,33 @@ - + - + - + - + - + - + - + - + - + - + @@ -174,17 +174,13 @@ - - created by - + - - creation date - + @@ -197,7 +193,7 @@ - has_broad_synonym + has_broad_synonym @@ -205,7 +201,7 @@ - database_cross_reference + database_cross_reference @@ -213,7 +209,7 @@ - has_exact_synonym + has_exact_synonym @@ -221,7 +217,7 @@ - has_narrow_synonym + has_narrow_synonym @@ -229,7 +225,7 @@ - has_obo_format_version + has_obo_format_version @@ -237,7 +233,7 @@ - has_obo_namespace + has_obo_namespace @@ -245,7 +241,7 @@ - has_related_synonym + has_related_synonym @@ -253,23 +249,21 @@ - has_synonym_type + has_synonym_type - - id - + - in_subset + in_subset @@ -283,7 +277,7 @@ - treat-xrefs-as-equivalent + treat-xrefs-as-equivalent @@ -337,10 +331,10 @@ - Imaging is a process that produces an image of something. - DPBO - AFP:0003774 - imaging + Imaging is a process that produces an image of something. + DPBO + AFP:0003774 + imaging @@ -348,16 +342,16 @@ - The date/time of the measurement. - DPBO - AFR:0000952 - measurement time + The date/time of the measurement. + DPBO + AFR:0000952 + measurement time - The date/time of the measurement. - Allotrope + The date/time of the measurement. + Allotrope @@ -365,16 +359,16 @@ - A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component. - DPBO - AFR:0001255 - temperature setting + A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component. + DPBO + AFR:0001255 + temperature setting - A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component. - Allotrope + A temperature setting is a setting that specifies some temperature configuration of a temperature controlling or monitoring device, that controls or monitors the target temperature at the site of some system component. + Allotrope @@ -382,10 +376,10 @@ - The injection volume setting is an injection setting that specifies the volume of the fluid to be injected. - DPBO - AFR:0001577 - injection volume setting + The injection volume setting is an injection setting that specifies the volume of the fluid to be injected. + DPBO + AFR:0001577 + injection volume setting @@ -393,10 +387,10 @@ - A sample temperature result is a quality quantification facet that quantifies the temperature of the sample. - DPBO - AFR:0002149 - sample temperature + A sample temperature result is a quality quantification facet that quantifies the temperature of the sample. + DPBO + AFR:0002149 + sample temperature @@ -404,10 +398,10 @@ - A planned process in which water is artificially supplied to plant or soil to sustain plants. - DPBO - AGRO:00000006 - irrigation process + A planned process in which water is artificially supplied to plant or soil to sustain plants. + DPBO + AGRO:00000006 + irrigation process @@ -416,12 +410,12 @@ - A pruning process in which one or more suckers are removed. - desuckering process - DPBO - AGRO:00000007 - Which suckers are removed depends on the criteria set by the agent of the desuckering process. - desuckering + A pruning process in which one or more suckers are removed. + desuckering process + DPBO + AGRO:00000007 + Which suckers are removed depends on the criteria set by the agent of the desuckering process. + desuckering @@ -430,20 +424,20 @@ - A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products. - https://orcid.org/0000-0001-6284-4821 - pruning - thinning process - DPBO - AGRO:00000027 - thinning + A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products. + https://orcid.org/0000-0001-6284-4821 + pruning + thinning process + DPBO + AGRO:00000027 + thinning - A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products. - http://aims.fao.org/aos/agrovoc/c_6274 - https://en.wikipedia.org/wiki/Pruning#Types_of_pruning + A planned process in which selected parts of the plant are removed. The practice entails targeted removal of diseased, damaged, dead, non-productive, structurally unsound, or otherwise unwanted tissue from plants. This is done in order to shape the plant or tree, improve plant or tree health, reduce the risk from falling branches, prepare nursery specimens for transplanting, and increase the yield or quality of harvested products. + http://aims.fao.org/aos/agrovoc/c_6274 + https://en.wikipedia.org/wiki/Pruning#Types_of_pruning @@ -451,10 +445,10 @@ - Location where the experiment is implemented. - DPBO - AGRO:00000360 - experimental site + Location where the experiment is implemented. + DPBO + AGRO:00000360 + experimental site @@ -463,10 +457,10 @@ - Experimental site in which the experiment is implemented on the field of a farmer. - DPBO - AGRO:00000361 - farmer field + Experimental site in which the experiment is implemented on the field of a farmer. + DPBO + AGRO:00000361 + farmer field @@ -475,11 +469,11 @@ - Experimental site in which the experiment is done in a the field of a research station. - experimental station field - DPBO - AGRO:00000362 - research station field + Experimental site in which the experiment is done in a the field of a research station. + experimental station field + DPBO + AGRO:00000362 + research station field @@ -488,19 +482,19 @@ - An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions. - hothouse - screenhouse - glasshouse - DPBO - AGRO:00000363 - greenhouse + An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions. + hothouse + screenhouse + glasshouse + DPBO + AGRO:00000363 + greenhouse - An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions. - https://en.wikipedia.org/wiki/Greenhouse + An experimental site in which the experiment is performed in a structure with walls and roof made chiefly of transparent material, such as glass, with the possibility to regulate climatic conditions. + https://en.wikipedia.org/wiki/Greenhouse @@ -509,10 +503,10 @@ - Experimental site where the experiment is done in a forest owned by a government. - DPBO - AGRO:00000364 - governmental forest + Experimental site where the experiment is done in a forest owned by a government. + DPBO + AGRO:00000364 + governmental forest @@ -521,10 +515,10 @@ - Experimental site where the experiment is done in a private forest. - DPBO - AGRO:00000365 - private forest + Experimental site where the experiment is done in a private forest. + DPBO + AGRO:00000365 + private forest @@ -533,10 +527,10 @@ - A person engaged in agriculture, raising living organisms for food or raw materials. - DPBO - AGRO:00000372 - farmer + A person engaged in agriculture, raising living organisms for food or raw materials. + DPBO + AGRO:00000372 + farmer @@ -545,11 +539,11 @@ - A person who conducts research. - scientist - DPBO - AGRO:00000373 - researcher + A person who conducts research. + scientist + DPBO + AGRO:00000373 + researcher @@ -558,11 +552,11 @@ - A person that is enrolled or attends classes at a school, college, or university. - DPBO - intern - AGRO:00000374 - student + A person that is enrolled or attends classes at a school, college, or university. + DPBO + intern + AGRO:00000374 + student @@ -571,10 +565,10 @@ - A person that works in a research station. - DPBO - AGRO:00000375 - research station employee + A person that works in a research station. + DPBO + AGRO:00000375 + research station employee @@ -583,10 +577,10 @@ - A person that is employed by the government to assist people in rural areas with methods of farming and home economics. - DPBO - AGRO:00000376 - extension agent + A person that is employed by the government to assist people in rural areas with methods of farming and home economics. + DPBO + AGRO:00000376 + extension agent @@ -595,10 +589,10 @@ - A person that is an educator who works at a college or university. - DPBO - AGRO:00000377 - faculty member + A person that is an educator who works at a college or university. + DPBO + AGRO:00000377 + faculty member @@ -606,10 +600,10 @@ - Roled performed by a person during an experiment. - DPBO - AGRO:00000378 - person role within the experiment + Roled performed by a person during an experiment. + DPBO + AGRO:00000378 + person role within the experiment @@ -618,10 +612,10 @@ - A person that has a role of collecting data related to the experiment. - DPBO - AGRO:00000379 - data collector + A person that has a role of collecting data related to the experiment. + DPBO + AGRO:00000379 + data collector @@ -630,10 +624,10 @@ - A person that is the holder of an independent grant and the lead researcher for the grant project. - DPBO - AGRO:00000380 - principal investigator + A person that is the holder of an independent grant and the lead researcher for the grant project. + DPBO + AGRO:00000380 + principal investigator @@ -642,10 +636,10 @@ - A person that has a role of managing the experiment. - DPBO - AGRO:00000381 - experiment manager + A person that has a role of managing the experiment. + DPBO + AGRO:00000381 + experiment manager @@ -654,10 +648,10 @@ - A person that has a role of performing the operations required to run the experiment in the field. - DPBO - AGRO:00000382 - field laborer + A person that has a role of performing the operations required to run the experiment in the field. + DPBO + AGRO:00000382 + field laborer @@ -666,19 +660,19 @@ - Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots. + Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots. - pruning - pruning method - DPBO - AGRO:00000566 - pruning process + pruning + pruning method + DPBO + AGRO:00000566 + pruning process - Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots. - https://en.wikipedia.org/wiki/Pruning + Process which involves the selective removal of certain parts of a plant or a tree, such as branches, buds, or roots. + https://en.wikipedia.org/wiki/Pruning @@ -686,21 +680,21 @@ - A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters + A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters - geographic coordinate system - GPS coordinates measurement datum - geo-location - geolocation - DPBO - AGRO:00000572 - GPS coordinates + geographic coordinate system + GPS coordinates measurement datum + geo-location + geolocation + DPBO + AGRO:00000572 + GPS coordinates - A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters - https://whatis.techtarget.com/definition/GPS-coordinates + A measurement datum that is a unique identifier of a precise geographic location on the earth, usually expressed in alphanumeric characters + https://whatis.techtarget.com/definition/GPS-coordinates @@ -709,10 +703,10 @@ - A person that own an agricultural field. - DPBO - AGRO:00000659 - field owner + A person that own an agricultural field. + DPBO + AGRO:00000659 + field owner @@ -720,11 +714,11 @@ - A planned process which occurs in an agricultural field. + A planned process which occurs in an agricultural field. - DPBO - AGRO:00002071 - agricultural process + DPBO + AGRO:00002071 + agricultural process @@ -732,11 +726,11 @@ - - DNA or deoxyribonucleic acid is the genetic material in all the living things, and some viruses. It is a polymer of nucleotides, with a backbone made of deoxyribose sugar and phosphate groups joined together by ester bonds. - DPBO - BAO:0000269 - DNA + + DNA or deoxyribonucleic acid is the genetic material in all the living things, and some viruses. It is a polymer of nucleotides, with a backbone made of deoxyribose sugar and phosphate groups joined together by ester bonds. + DPBO + BAO:0000269 + DNA @@ -744,11 +738,11 @@ - - DNA that is linear and not circular. Examples of linear DNA include synthetic oligonucleotide, restriction endonuclease digestion product, polymerase chain reaction product, mechanically sheared genomic DNA, etc. - DPBO - BAO:0000316 - genomic DNA + + DNA that is linear and not circular. Examples of linear DNA include synthetic oligonucleotide, restriction endonuclease digestion product, polymerase chain reaction product, mechanically sheared genomic DNA, etc. + DPBO + BAO:0000316 + genomic DNA @@ -756,10 +750,10 @@ - This microplate contains 96 wells. It is suitable for a low throughput assay. - DPBO - BAO:0000513 - 96 well plate + This microplate contains 96 wells. It is suitable for a low throughput assay. + DPBO + BAO:0000513 + 96 well plate @@ -767,10 +761,10 @@ - The role of a company as a creator of detection instrumentation. - DPBO - BAO:0002628 - instrumentation manufacturer + The role of a company as a creator of detection instrumentation. + DPBO + BAO:0002628 + instrumentation manufacturer @@ -779,9 +773,9 @@ - DPBO - BAO:0010013 - 6 well plate + DPBO + BAO:0010013 + 6 well plate @@ -789,13 +783,13 @@ - Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications - protein profiling - protein quantification assay - protein quantification assay - DPBO - BAO:0010026 - protein profiling assay + Protein profiling assays can be used to identify and quantify proteins together with their post-translational modifications + protein profiling + protein quantification assay + protein quantification assay + DPBO + BAO:0010026 + protein profiling assay @@ -804,10 +798,10 @@ - An assay that is used to identify in a data-dependent mode proteins by combining the HPLC and MS methods. It is also known as liquid chromatography-coupled tandem mass spectrometry (LC-MS) - DPBO - BAO:0010027 - shotgun MS protein profiling assay + An assay that is used to identify in a data-dependent mode proteins by combining the HPLC and MS methods. It is also known as liquid chromatography-coupled tandem mass spectrometry (LC-MS) + DPBO + BAO:0010027 + shotgun MS protein profiling assay @@ -816,10 +810,10 @@ - Sequential window acquisition of all theoretical mass spectra (SWATH) MS is a mass spectrometrical method thatcouples data-independent acquisition is coupled with peptide spectral library match - DPBO - BAO:0010028 - SWATH MS protein profiling assay + Sequential window acquisition of all theoretical mass spectra (SWATH) MS is a mass spectrometrical method thatcouples data-independent acquisition is coupled with peptide spectral library match + DPBO + BAO:0010028 + SWATH MS protein profiling assay @@ -828,10 +822,10 @@ - A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes - DPBO - BAO:0010029 - P100 protein profiling assay + A targeted phosphoproteomic assay that uses a data-driven approach to identify and quantify a set of 96 phosphopeptide probes + DPBO + BAO:0010029 + P100 protein profiling assay @@ -840,10 +834,10 @@ - Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies - DPBO - BAO:0010030 - RPPA protein profiling assay + Reverse phase protein array (RPPA) is a an assay that measures multiple protein expression levels in a large number of biological samples simultaneously using high quality antibodies + DPBO + BAO:0010030 + RPPA protein profiling assay @@ -852,9 +846,9 @@ - DPBO - BAO:0010049 - Microwestern + DPBO + BAO:0010049 + Microwestern @@ -863,9 +857,9 @@ - DPBO - BAO:0010052 - ELISA protein state assay + DPBO + BAO:0010052 + ELISA protein state assay @@ -874,9 +868,9 @@ - DPBO - BAO:0010070 - Tandem Mass Tag (TMT) MS Protein Quantification + DPBO + BAO:0010070 + Tandem Mass Tag (TMT) MS Protein Quantification @@ -885,9 +879,9 @@ - DPBO - BAO:0010071 - Liquid Chromatography/Mass Spectroscopy (LC/MS) protein quantification + DPBO + BAO:0010071 + Liquid Chromatography/Mass Spectroscopy (LC/MS) protein quantification @@ -896,16 +890,16 @@ - A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. - BrendaTissueOBO - BTO:0001899 - stationary phase culture + A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. + BrendaTissueOBO + BTO:0001899 + stationary phase culture - A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. - Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Stationary+phase + A cell culture at the plateau of the growth curve after log growth in a culture, during which cell number remains constant. New cells are produced at the same rate as older cells die. + Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Stationary+phase @@ -913,16 +907,16 @@ - The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. - BrendaTissueOBO - BTO:0001900 - growth phase culture + The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. + BrendaTissueOBO + BTO:0001900 + growth phase culture - The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. - Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Growth+phase + The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. + Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Growth+phase @@ -931,16 +925,16 @@ - A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases. - BrendaTissueOBO - BTO:0001901 - death phase culture + A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases. + BrendaTissueOBO + BTO:0001901 + death phase culture - A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases. - Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Death+phase + A cell culture at the final growth phase in a culture, during which nutrients have been depleted and cell number decreases. + Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Death+phase @@ -949,16 +943,16 @@ - The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth. - BrendaTissueOBO - BTO:0001902 - lag phase culture + The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth. + BrendaTissueOBO + BTO:0001902 + lag phase culture - The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth. - Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Lag+phase + The culture at the initial growth phase, during which cell number remains relatively constant prior to rapid growth. + Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Lag+phase @@ -967,18 +961,18 @@ - A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. - BrendaTissueOBO - exponential growth phase culture - log phase culture - BTO:0001903 - logarithmic phase culture + A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. + BrendaTissueOBO + exponential growth phase culture + log phase culture + BTO:0001903 + logarithmic phase culture - A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. - Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Logarithmic+phase + A cell culture at the steepest slope of the growth curve of a culture-- at the phase of vigorous growth during which cell number doubles every 20-30 minutes. + Biology_Dictionary_Hyperdictionary:http://www.hyperdictionary.com/dictionary/Logarithmic+phase @@ -986,11 +980,11 @@ - - biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. - DPBO - CHEBI:36080 - protein + + biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. + DPBO + CHEBI:36080 + protein @@ -998,10 +992,10 @@ - A fluid that percolates through or along the stationary bed in chromatography. - DPBO - CHMO:0000995 - mobile phase + A fluid that percolates through or along the stationary bed in chromatography. + DPBO + CHMO:0000995 + mobile phase @@ -1010,17 +1004,17 @@ - The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc. - derivatization - DPBO - CHMO:0001485 - derivatisation + The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc. + derivatization + DPBO + CHMO:0001485 + derivatisation - The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc. - https://orcid.org/0000-0002-0640-0422 + The transformation of a chemical compound (the 'educt') into another similar compound (the 'derivative') by altering one or more of its functional groups. Derivatisation is generally perfomed to alter reactivity or change a physical property such as solubility, boiling point, melting point, thermal stability etc. + https://orcid.org/0000-0002-0640-0422 @@ -1029,23 +1023,23 @@ - The process of removing a solvent from a substance. - DPBO - drying - CHMO:0001549 - sample drying + The process of removing a solvent from a substance. + DPBO + drying + CHMO:0001549 + sample drying - The process of removing a solvent from a substance. - https://orcid.org/0000-0002-0640-0422 + The process of removing a solvent from a substance. + https://orcid.org/0000-0002-0640-0422 - drying - + drying + @@ -1054,16 +1048,16 @@ - The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature. - DPBO - CHMO:0001557 - vacuum drying + The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature. + DPBO + CHMO:0001557 + vacuum drying - The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature. - https://orcid.org/0000-0002-0640-0422 + The removal of water from a sample by placing it under reduced pressure. This allows water to evaporate from (heat-sensitive) samples at a lower temperature. + https://orcid.org/0000-0002-0640-0422 @@ -1071,10 +1065,10 @@ - The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it. - DPBO - CHMO:0001577 - extraction + The transfer of a solute from a liquid phase to another immiscible or partially-miscible liquid phase in contact with it. + DPBO + CHMO:0001577 + extraction @@ -1082,35 +1076,35 @@ - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles). - liquid-solid extraction - solid phase extraction - solid-phase extraction - sorbent extraction - sorptive extraction - DPBO - LSE - SPE - CHMO:0001583 - liquid-solid extraction + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles). + liquid-solid extraction + solid phase extraction + solid-phase extraction + sorbent extraction + sorptive extraction + DPBO + LSE + SPE + CHMO:0001583 + liquid-solid extraction - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles). - ISBN:0-13-147835-4 + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (e.g. silica particles). + ISBN:0-13-147835-4 - LSE - + LSE + - SPE - + SPE + @@ -1119,19 +1113,19 @@ - The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase. - normal phase SPE - normal phase solid-phase extraction - normal-phase SPE - DPBO - CHMO:0001584 - normal-phase solid-phase extraction + The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase. + normal phase SPE + normal phase solid-phase extraction + normal-phase SPE + DPBO + CHMO:0001584 + normal-phase solid-phase extraction - The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase. - ISBN:0-13-147835-4 + The process of transferring a substance from a liquid to a solid phase by passing the (polar) liquid sample through a (non-polar) stationary phase. + ISBN:0-13-147835-4 @@ -1140,22 +1134,22 @@ - The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase. - reverse phase SPE - reverse phase solid-phase extraction - reverse-phase SPE - reverse-phase solid-phase extraction - reversed phase SPE - reversed-phase SPE - DPBO - CHMO:0001585 - reversed-phase solid-phase extraction + The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase. + reverse phase SPE + reverse phase solid-phase extraction + reverse-phase SPE + reverse-phase solid-phase extraction + reversed phase SPE + reversed-phase SPE + DPBO + CHMO:0001585 + reversed-phase solid-phase extraction - The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase. - ISBN:0-13-147835-4 + The process of transferring a substance from a liquid to a solid phase by passing the (non-polar) liquid sample through a (polar) stationary phase. + ISBN:0-13-147835-4 @@ -1164,19 +1158,19 @@ - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter). - SPME - solid phase microextraction - solid-phase microextraction - DPBO - CHMO:0001586 - solid-phase micro-extraction + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter). + SPME + solid phase microextraction + solid-phase microextraction + DPBO + CHMO:0001586 + solid-phase micro-extraction - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter). - ISBN:0-13-147835-4 + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter). + ISBN:0-13-147835-4 @@ -1185,18 +1179,18 @@ - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary. - CME - capillary microextraction - DPBO - CHMO:0001587 - capillary micro-extraction + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary. + CME + capillary microextraction + DPBO + CHMO:0001587 + capillary micro-extraction - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary. - ISBN:0444505113 + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small fused-silica capillary. + ISBN:0444505113 @@ -1205,22 +1199,22 @@ - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary. - sgCME - sol-gel CME - sol-gel capillary micro-extraction - sol-gel capillary microextraction - solgel CME - solgel capillary microextraction - DPBO - CHMO:0001588 - sol–gel capillary micro-extraction + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary. + sgCME + sol-gel CME + sol-gel capillary micro-extraction + sol-gel capillary microextraction + solgel CME + solgel capillary microextraction + DPBO + CHMO:0001588 + sol–gel capillary micro-extraction - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary. - https://doi.org/10.1021/ac0109523 + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a small sol–gel-coated fused-silica capillary. + https://doi.org/10.1021/ac0109523 @@ -1229,22 +1223,22 @@ - The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample. - HSPME - HSSE - hSPME - headspace solid-phase micro-extraction - headspace solid-phase microextraction - headspace sorptive extraction - DPBO - CHMO:0001589 - headspace solid-phase micro-extraction + The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample. + HSPME + HSSE + hSPME + headspace solid-phase micro-extraction + headspace solid-phase microextraction + headspace sorptive extraction + DPBO + CHMO:0001589 + headspace solid-phase micro-extraction - The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample. - https://orcid.org/0000-0002-0640-0422 + The process of transferring a substance from a liquid to a solid phase by exposing a small fibre containing a stationary phase bonded to a silica needle (<10 μm diameter) to the headspace above the liquid sample. + https://orcid.org/0000-0002-0640-0422 @@ -1253,25 +1247,25 @@ - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe. - MEPS - micro extraction by packed sorbent - micro-extraction in packed syringe - microextraction in a packed syringe - microextraction in packed syringe - packed syringe micro-extraction - packed syringe microextraction - packed-syringe micro-extraction - packed-syringe microextraction - DPBO - CHMO:0001590 - micro-extraction in a packed syringe + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe. + MEPS + micro extraction by packed sorbent + micro-extraction in packed syringe + microextraction in a packed syringe + microextraction in packed syringe + packed syringe micro-extraction + packed syringe microextraction + packed-syringe micro-extraction + packed-syringe microextraction + DPBO + CHMO:0001590 + micro-extraction in a packed syringe - The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe. - https://doi.org/10.1002/jms.73 + The process of transferring a substance from a liquid to a solid phase by passing the liquid sample through a stationary phase (1 mg) packed into a microlitre syringe. + https://doi.org/10.1002/jms.73 @@ -1280,16 +1274,16 @@ - The process of transferring a substance from any matrix to an appropriate liquid phase. - DPBO - CHMO:0001598 - solvent extraction + The process of transferring a substance from any matrix to an appropriate liquid phase. + DPBO + CHMO:0001598 + solvent extraction - The process of transferring a substance from any matrix to an appropriate liquid phase. - OrangeBook:9.4.1 + The process of transferring a substance from any matrix to an appropriate liquid phase. + OrangeBook:9.4.1 @@ -1298,20 +1292,20 @@ - The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. - dry grinding - milling - solid-state grinding - solvent-free grinding - DPBO - CHMO:0001652 - grinding + The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. + dry grinding + milling + solid-state grinding + solvent-free grinding + DPBO + CHMO:0001652 + grinding - The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. - https://doi.org/10.1351/goldbook.M03928 + The mechanical reduction of the particle size of a solid sample by attribution (friction), impact or cutting. + https://doi.org/10.1351/goldbook.M03928 @@ -1320,20 +1314,20 @@ - - Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. - methoxyamination derivatization - DPBO - CHMO:0002757 - this typically happens prior to GC-MS, but not LC-MS - methoxyamination derivatisation + + Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. + methoxyamination derivatization + DPBO + CHMO:0002757 + this typically happens prior to GC-MS, but not LC-MS + methoxyamination derivatisation - Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. - https://doi.org/10.1039/9781847558107-00254 - https://orcid.org/0000-0001-5985-7429 + Derivatisation of a metabolite by addition of pyridinic methoxyamine to stabilise carbonyl moieties. + https://doi.org/10.1039/9781847558107-00254 + https://orcid.org/0000-0001-5985-7429 @@ -1342,21 +1336,21 @@ - - Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. - TMS derivatisation - trimethylsilyl derivatization - DPBO - CHMO:0002758 - this typically happens prior to GC-MS, but not LC-MS - trimethylsilyl derivatisation + + Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. + TMS derivatisation + trimethylsilyl derivatization + DPBO + CHMO:0002758 + this typically happens prior to GC-MS, but not LC-MS + trimethylsilyl derivatisation - Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. - https://doi.org/10.1039/9781847558107-00254 - https://orcid.org/0000-0001-5985-7429 + Derivatisation of a metabolite by addition of a trimethylsilyl reagent to protect functional groups such as hydroxy, carboxylic acid, thio and amine groups. + https://doi.org/10.1039/9781847558107-00254 + https://orcid.org/0000-0001-5985-7429 @@ -1365,10 +1359,10 @@ - dispersive solid-phase extraction - DPBO - CHMO:0002863 - dispersive solid phase extraction + dispersive solid-phase extraction + DPBO + CHMO:0002863 + dispersive solid phase extraction @@ -1377,4972 +1371,4972 @@ - DPBO - CHMO:0002887 - dispersive solid-phase microextraction + DPBO + CHMO:0002887 + dispersive solid-phase microextraction - + - - - A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted - DPBO - Experimental Randomisation - DPBO:0000001 - growth plot design + + + A plan specification that states how treatments are allocated to the experimental units. It refers to the conceptual framework within which the experiment is conducted + DPBO + Experimental Randomisation + DPBO:0000001 + growth plot design - + - - The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478 - DPBO - DPBO:0000002 - “We might need to add the relationship with the class referenced above” - read alignment software + + The software used for read alignment i.e http://edamontology.org/operation_3198 or http://purl.obolibrary.org/obo/OBI_0002478 + DPBO + DPBO:0000002 + “We might need to add the relationship with the class referenced above” + read alignment software - + - - The version of the read alignment software (DPBO:0000002). - DPBO - DPBO:0000003 - read alignment software version + + The version of the read alignment software (DPBO:0000002). + DPBO + DPBO:0000003 + read alignment software version - + - - The parameters of the read alignment software (DPBO:0000002). - DPBO - DPBO:0000004 - read alignment software parameters + + The parameters of the read alignment software (DPBO:0000002). + DPBO + DPBO:0000004 + read alignment software parameters - + - - This term defines the relative humidity of the air at daytime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) - DPBO - DPBO:0000005 - "is_a: http://purl.obolibrary.org/obo/PECO_0007197" - humidity day + + This term defines the relative humidity of the air at daytime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) + DPBO + DPBO:0000005 + "is_a: http://purl.obolibrary.org/obo/PECO_0007197" + humidity day - + - - This term defines the relative humidity of the air at nighttime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) - DPBO - DPBO:0000006 - "is_a: http://purl.obolibrary.org/obo/PECO_0007197" - humidity night + + This term defines the relative humidity of the air at nighttime, it is a specialised concept of humidity exposure (http://purl.obolibrary.org/obo/PECO_0007197) + DPBO + DPBO:0000006 + "is_a: http://purl.obolibrary.org/obo/PECO_0007197" + humidity night - + - - This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) - DPBO - DPBO:0000007 - “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” - temperature day + + This term defines the air temperature at daytime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) + DPBO + DPBO:0000007 + “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” + temperature day - + - - This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) - DPBO - DPBO:0000008 - “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” - temperature night + + This term defines the air temperature at nighttime, it is a specialised concept of temperature of air (http://purl.obolibrary.org/obo/ENVO_09200001) + DPBO + DPBO:0000008 + “is_a: http://purl.obolibrary.org/obo/ENVO_09200001” + temperature night - + - - Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ” - DPBO - DPBO:0000009 - sample collection method + + Details of method to gather (e.g. scissors, scalpel) or pool the sample, tissue, organ” + DPBO + DPBO:0000009 + sample collection method - + - - Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.” - DPBO - DPBO:0000010 - “” - metabolism quenching method + + Method used to stop the metabolism in the sample (e.g. shock-freeze in liquid nitrogen). May include the time passed since sample collection.” + DPBO + DPBO:0000010 + “” + metabolism quenching method - + - - The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample” - DPBO - DPBO:0000011 - “” - sample storage + + The method used for sample storage. Should include the temperature of the sample. May include the medium (freezer or liquid nitrogen) and/or additional processing (freeze-drying) of the sample” + DPBO + DPBO:0000011 + “” + sample storage - + - - The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.” - DPBO - DPBO:0000012 - “” - bio entity + + The biological entity (e.g. RNA, DNA, metabolites, proteins, lipids) to be extracted from a biosource targeted for assay / measurement.” + DPBO + DPBO:0000012 + “” + bio entity - + - - The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.” - DPBO - DPBO:0000013 - “” - biosource amount + + The amount (typically in milligram) of material from which a bio entity (DPBO:0000012) is extracted.” + DPBO + DPBO:0000013 + “” + biosource amount - + - - The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.” - DPBO - DPBO:0000014 - “” - extraction kit + + The name of the commercial kit used for extraction of a bio entity (DPBO:0000012). Should include the company name.” + DPBO + DPBO:0000014 + “” + extraction kit - + - - Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment” - DPBO - DPBO:0000015 - “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423" - library layout + + Determines the choice of DNA sequencing strategy, in which a single read is initiated from each end (paired-end) or one end (single-end) of DNA fragment” + DPBO + DPBO:0000015 + “Adapted from http://purl.obolibrary.org/obo/NCIT_C150423" + library layout - + - - Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)” - DPBO - DPBO:0000016 - “” - library RNA amount + + Amount of RNA (typically microgram) used as starting material for library construction (http://purl.obolibrary.org/obo/GENEPIO_0001994)” + DPBO + DPBO:0000016 + “” + library RNA amount - + - - The name of the software used for base-calling. - DPBO - DPBO:0000017 - term description for base-calling http://edamontology.org/operation_3185 - base-calling software + + The name of the software used for base-calling. + DPBO + DPBO:0000017 + term description for base-calling http://edamontology.org/operation_3185 + base-calling software - + - - The version of the base-calling software (DPBO:0000017).” - DPBO - DPBO:0000018 - “” - base-calling software version + + The version of the base-calling software (DPBO:0000017).” + DPBO + DPBO:0000018 + “” + base-calling software version - + - - The parameters of the base-calling software (DPBO:0000017).” - DPBO - DPBO:0000019 - “” - base-calling software parameters + + The parameters of the base-calling software (DPBO:0000017).” + DPBO + DPBO:0000019 + “” + base-calling software parameters - + - - Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)” - DPBO - DPBO:0000020 - “” - library strand + + Determines the read direction. Only applies to nucleotide sequencing in paired-end layout (DPBO:0000015)” + DPBO + DPBO:0000020 + “” + library strand - + - - File format of the raw data file” - DPBO - DPBO:0000021 - “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915" - raw data file format + + File format of the raw data file” + DPBO + DPBO:0000021 + “This is a specialization of https://ifb-elixirfr.github.io/edam-browser/#http://edamontology.org/format_1915" + raw data file format - + - - Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum - DPBO - DPBO:0000022 - raw data file checksum + + Checksum of the raw data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum + DPBO + DPBO:0000022 + raw data file checksum - + - - Name of the software applied for data filtering - DPBO - DPBO:0000023 - “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)” - data filtering software + + Name of the software applied for data filtering + DPBO + DPBO:0000023 + “For RNA-seq data, this may be a read adapter trimming software (GENEPIO_0002096)” + data filtering software - + - - The version of the data filtering software (DPBO:0000023).” - DPBO - DPBO:0000024 - “” - data filtering software version + + The version of the data filtering software (DPBO:0000023).” + DPBO + DPBO:0000024 + “” + data filtering software version - + - - The parameters of the data filtering software (DPBO:0000023).” - DPBO - DPBO:0000025 - “” - data filtering software parameters + + The parameters of the data filtering software (DPBO:0000023).” + DPBO + DPBO:0000025 + “” + data filtering software parameters - + - - Name and version of the genome reference.” - MS:1002644 - NCIT:C16438 - DPBO - DPBO:0000026 - “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644” - genome reference sequence + + Name and version of the genome reference.” + MS:1002644 + NCIT:C16438 + DPBO + DPBO:0000026 + “See also http://purl.obolibrary.org/obo/NCIT_C164388 and http://purl.obolibrary.org/obo/MS_1002644” + genome reference sequence - + - - File format of the processed data file” - DPBO - DPBO:0000027 - “” - processed data file format + + File format of the processed data file” + DPBO + DPBO:0000027 + “” + processed data file format - + - - Name of the processed data file” - DPBO - DPBO:0000028 - “” - processed data file name + + Name of the processed data file” + DPBO + DPBO:0000028 + “” + processed data file name - + - - Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum - DPBO - DPBO:0000029 - processed data file checksum + + Checksum of the processed data file, it is a specialised concept of http://purl.obolibrary.org/obo/NCIT_C43522” ! Checksum + DPBO + DPBO:0000029 + processed data file checksum - + - - Publication reference for isolation and growth condition specifications of the organism/material - DPBO - DPBO:0000030 - for submission to ENA - isolation and growth condition + + Publication reference for isolation and growth condition specifications of the organism/material + DPBO + DPBO:0000030 + for submission to ENA + isolation and growth condition - + - - The haploid chromosome count of a eukaryote - DPBO - DPBO:0000031 - number of chromosomes + + The haploid chromosome count of a eukaryote + DPBO + DPBO:0000031 + number of chromosomes - + - - The estimated size of the genome prior to sequencing - DPBO - DPBO:0000032 - adapted from MIXS:0000024 - estimated genome size + + The estimated size of the genome prior to sequencing + DPBO + DPBO:0000032 + adapted from MIXS:0000024 + estimated genome size - + - - A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). - DPBO - DPBO:0000033 - “This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)" - plant age + + A temporal measurement of the time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise the identifiable point must be specified such as planting (e.g. 3 days post planting). + DPBO + DPBO:0000033 + “This is a specialization of age (http://www.ebi.ac.uk/efo/EFO_0000246)" + plant age - + - - Health status of the plant at the time of sample collection - DPBO - DPBO:0000034 - plant health state + + Health status of the plant at the time of sample collection + DPBO + DPBO:0000034 + plant health state - + - - - Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. - DPBO - DPBO:0000035 - obsolete_Seurat + + + Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. + DPBO + DPBO:0000035 + obsolete_Seurat true - + - - - The method used to select for or against, enrich, or screen the material being sequenced. - GENEPIO:0001940 - DPBO - DPBO:0000036 - term is redundant, please use GENEPIO:0001940 - obsolete_library selection + + + The method used to select for or against, enrich, or screen the material being sequenced. + GENEPIO:0001940 + DPBO + DPBO:0000036 + term is redundant, please use GENEPIO:0001940 + obsolete_library selection true - + - - Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line - DPBO - DPBO:0000037 - subspecific taxonomic rank + + Determination of the taxonomic ranking that is below species level i.e. variety, cultivar, ecotype, inbred line + DPBO + DPBO:0000037 + subspecific taxonomic rank - + - - pH measurement of the culture rooting medium - DPBO - DPBO:0000038 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium pH + + pH measurement of the culture rooting medium + DPBO + DPBO:0000038 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium pH - + - - Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L) - DPBO - DPBO:0000039 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium macronutrients + + Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170mg/L) + DPBO + DPBO:0000039 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium macronutrients - + - - Model name or number of next generation sequencing instrument - EFO:0003739 - DPBO - DPBO:0000040 - next generation sequencing instrument model + + Model name or number of next generation sequencing instrument + EFO:0003739 + DPBO + DPBO:0000040 + next generation sequencing instrument model - + - - The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day) - PECO:0007078 - ZECO:0000147 + + The time (e.g. hours of light) of the light regime in a growth experiment (e.g. 12hr light /12hr dark, 12/12, short day, long day) + PECO:0007078 + ZECO:0000147 - light duration - DPBO - DPBO:0000041 - “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078" - growth day length + light duration + DPBO + DPBO:0000041 + “Adapted from 'light quantity exposure' http://purl.obolibrary.org/obo/PECO_0007078" + growth day length - + - - Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2') - MS:1001809 - DPBO - DPBO:0000042 - biological replicate + + Indicates the biological replication during experiment design (e.g. 'rep1', 'rep2') + MS:1001809 + DPBO + DPBO:0000042 + biological replicate - + - - Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection) - DPBO - DPBO:0000043 - MS sample post-extraction + + Specific to metabolomic mass spectrometry assays. Steps performed after sample extraction (e.g. dried in a vacuum concentrator, solid phase microextraction direct injection) + DPBO + DPBO:0000043 + MS sample post-extraction - + - - Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile) - DPBO - DPBO:0000044 - MS sample resuspension + + Specific to metabolomic mass spectrometry assays. Resuspension after sample extraction (e.g. dried samples resuspended in pyridine, dried samples resuspended in acetonitrile) + DPBO + DPBO:0000044 + MS sample resuspension - + - - Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control) - DPBO - DPBO:0000045 - MS sample type + + Specific to metabolomic mass spectrometry assays. Type of sample (e.g. experimental sample, pooled sample, blank, medium blank, retention index, reference standard, quality control) + DPBO + DPBO:0000045 + MS sample type - + - - Company name, and instrument name or serial number of the chromatography instrument - DPBO - DPBO:0000046 - chromatography instrument model + + Company name, and instrument name or serial number of the chromatography instrument + DPBO + DPBO:0000046 + chromatography instrument model - + - - Company name, and name or serial number of the chromatography autosampler model - DPBO - DPBO:0000047 - chromatography autosampler model + + Company name, and name or serial number of the chromatography autosampler model + DPBO + DPBO:0000047 + chromatography autosampler model - + - - Company name, and name or serial number of the chromatography column - DPBO - DPBO:0000048 - chromatography column model + + Company name, and name or serial number of the chromatography column + DPBO + DPBO:0000048 + chromatography column model - + - - Company name, and name or serial number of the chromatography guard column - DPBO - DPBO:0000049 - chromatography guard column model + + Company name, and name or serial number of the chromatography guard column + DPBO + DPBO:0000049 + chromatography guard column model - + - - Chemical buffer, solvent or solution used to extract a component from a biological sample. - DPBO - DPBO:0000050 - “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB" - extraction buffer + + Chemical buffer, solvent or solution used to extract a component from a biological sample. + DPBO + DPBO:0000050 + “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884). DB" + extraction buffer - + - - Volume of the buffer (DPBO:0000050) used during extraction. - DPBO - DPBO:0000051 - “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)" - extraction buffer volume + + Volume of the buffer (DPBO:0000050) used during extraction. + DPBO + DPBO:0000051 + “related to extraction (http://purl.obolibrary.org/obo/OBI_0302884)" + extraction buffer volume - + - + - Derivatization for metabolomics mass spectrometry. - CHMO:0001485 - DPBO - DPBO:0000052 - MS derivatization + Derivatization for metabolomics mass spectrometry. + CHMO:0001485 + DPBO + DPBO:0000052 + MS derivatization - + - - Type of chromatography column (DPBO:0000048) - CHMO:0001000 - DPBO - DPBO:0000053 - chromatography column type + + Type of chromatography column (DPBO:0000048) + CHMO:0001000 + DPBO + DPBO:0000053 + chromatography column type - + - - Method or kit that was used to extract DNA or RNA - DPBO - DPBO:0000054 - “More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction" - extraction method + + Method or kit that was used to extract DNA or RNA + DPBO + DPBO:0000054 + “More general than DPBO:0000014, because not everyone uses a kit for RNA/DNA extraction" + extraction method - + - - Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L) - DPBO - DPBO:0000055 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium micronutrients + + Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2mg/L) + DPBO + DPBO:0000055 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium micronutrients - + - - Amount of DNA (microgram) used as starting material for library construction - DPBO - DPBO:0000056 - “" - library DNA amount + + Amount of DNA (microgram) used as starting material for library construction + DPBO + DPBO:0000056 + “" + library DNA amount - + - - Name of the company that produces next generation sequencing instruments - GENEPIO:0000071 - DPBO - DPBO:0000057 - next generation sequencing platform + + Name of the company that produces next generation sequencing instruments + GENEPIO:0000071 + DPBO + DPBO:0000057 + next generation sequencing platform - + - - Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L) - DPBO - DPBO:0000058 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium organic supplements + + Organic supplements of the culture rooting medium, such as vitaimins, amino acids, organic acids, antibiotics activated charcoal; e.g. Nicotinic acid (0.5mg/L) + DPBO + DPBO:0000058 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium organic supplements - + - - Strategy that was used to assemble reads into contigs - GENEPIO:0000090 - DPBO - DPBO:0000059 - “Just two options should be possible: de-novo assembly or mapping" - sequence assembly method + + Strategy that was used to assemble reads into contigs + GENEPIO:0000090 + DPBO + DPBO:0000059 + “Just two options should be possible: de-novo assembly or mapping" + sequence assembly method - + - - The version of the sequence assembly algorithm (OBI_0001522) - DPBO - DPBO:0000060 - “" - sequence assembly algorithm version + + The version of the sequence assembly algorithm (OBI_0001522) + DPBO + DPBO:0000060 + “" + sequence assembly algorithm version - + - - Status of the genome sequence that is uploaded - DPBO - DPBO:0000061 - “Just two options should be possible: full or partial" - genome status + + Status of the genome sequence that is uploaded + DPBO + DPBO:0000061 + “Just two options should be possible: full or partial" + genome status - + - - Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis. - DPBO - DPBO:0000062 - RNA quality check + + Measure of RNA quality after RNA extraction. Typically RNA integrity number (RIN) as provided by Agilent BioAnalyzer. Alternatively, RNA integrity checked via gel electrophoresis. + DPBO + DPBO:0000062 + RNA quality check - + - - The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345. - NCIT:C175890 - DPBO - DPBO:0000063 - “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" - BioProject accession number + + The accession number of the BioProject(s) to which the BioSample belongs. If the BioSample belongs to more than one BioProject, enter multiple bioproject_accession columns. A valid BioProject accession has prefix PRJN, PRJE or PRJD, e.g., PRJNA12345. + NCIT:C175890 + DPBO + DPBO:0000063 + “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" + BioProject accession number - + - - Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly - NCIT:C70713 - DPBO - DPBO:0000064 - “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" - sample type + + Sample type, such as cell culture, mixed culture, tissue sample, whole organism, single cell, metagenomic assembly + NCIT:C70713 + DPBO + DPBO:0000064 + “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" + sample type - + - - Source of organic carbon in the culture rooting medium; e.g. sucrose - DPBO - DPBO:0000065 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium carbon source + + Source of organic carbon in the culture rooting medium; e.g. sucrose + DPBO + DPBO:0000065 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium carbon source - + - - Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA - DPBO - DPBO:0000066 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium growth regulators + + Growth regulators in the culture rooting medium, such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5mg/L NAA + DPBO + DPBO:0000066 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium growth regulators - + - - Specification of the solidifying agent in the culture rooting medium; e.g. agar - DPBO - DPBO:0000067 - adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist - rooting medium solidifier + + Specification of the solidifying agent in the culture rooting medium; e.g. agar + DPBO + DPBO:0000067 + adapted from the ENA (European Nucleotide Archive) Plant Sample Checklist + rooting medium solidifier - + - - - A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ] - NCIT:C16403 - DPBO - DPBO:0000068 - “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]" - obsolete_cell line + + + A permanently established cell culture that will proliferate indefinitely given appropriate fresh medium and space. [ NCI On-line Medical Dictionary ] + NCIT:C16403 + DPBO + DPBO:0000068 + “[Definition Source: http://purl.obolibrary.org/obo/NCIT_C16403]" + obsolete_cell line true - + - - - The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI] - DPBO - DPBO:0000069 - term is redundant, please use NCIT:C12508 - obsolete_cell type + + + The smallest units of living structure capable of independent existence, composed of a membrane-enclosed mass of protoplasm and containing a nucleus or nucleoid. [Definition Source: NCI] + DPBO + DPBO:0000069 + term is redundant, please use NCIT:C12508 + obsolete_cell type true - + - - Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence. - DPBO - DPBO:0000070 - adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. - 5' partial CDS + + Incomplete CDS (coding sequence) with the start codon upstream of the submitted sequence. + DPBO + DPBO:0000070 + adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. + 5' partial CDS - + - - Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence. - DPBO - DPBO:0000071 - adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. - 3' partial CDS + + Incomplete CDS (coding sequence) with the stop codon downstream of the submitted sequence. + DPBO + DPBO:0000071 + adapted from the ENA (European Nucleotide Archive) CDS templates for annotated sequences. + 3' partial CDS - + - - Stage of plant disease at the time of sampling. - DPBO - DPBO:0000072 - plant disease stage + + Stage of plant disease at the time of sampling. + DPBO + DPBO:0000072 + plant disease stage - + - - Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601 - NCIT:C16977 - DPBO - DPBO:0000073 - “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" - phenotype + + Phenotype of sampled organism. For Phenotypic quality Ontology (PATO) (v1.269) terms, please see http://bioportal.bioontology.org/visualize/44601 + NCIT:C16977 + DPBO + DPBO:0000073 + “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" + phenotype - + - - Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps' - NCIT:C16632 - DPBO - DPBO:0000074 - “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" - geographic area + + Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg 'Canada: Vancouver' or 'Germany: halfway down Zugspitze, Alps' + NCIT:C16632 + DPBO + DPBO:0000074 + “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" + geographic area - + - - Incomplete promoter with its 5' end upstream of the submitted sequence. - DPBO - DPBO:0000075 - adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. - 5' partial promoter + + Incomplete promoter with its 5' end upstream of the submitted sequence. + DPBO + DPBO:0000075 + adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. + 5' partial promoter - + - - Incomplete promoter with its 3' end downstream of the submitted sequence. - DPBO - DPBO:0000076 - adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. - 3' partial promoter + + Incomplete promoter with its 3' end downstream of the submitted sequence. + DPBO + DPBO:0000076 + adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. + 3' partial promoter - + - - metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title - DPBO - DPBO:0000077 - “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title" - metabolite assignment file + + metabolite assignment file (MAF) as required by MetaboLights to describe metabolites analyzed during a metabolomics assay. Details see: https://www.ebi.ac.uk/metabolights/guides/MAF/Title + DPBO + DPBO:0000077 + “[Definition Source: https://www.ebi.ac.uk/metabolights/guides/MAF/Title" + metabolite assignment file - + - - BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]! - NCIT:C175889 - DPBO - DPBO:0000078 - “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" - BioSample accession number + + BioSample accession as required by NCBI repositories. Typically of the form SAMN[number]. NOT SUB[number]! + NCIT:C175889 + DPBO + DPBO:0000078 + “[Definition Source: taken from a template at https://www.ncbi.nlm.nih.gov/biosample/]" + BioSample accession number - + - - Coordinate of the 5' end of the promoter within the submitted sequence. - DPBO - DPBO:0000079 - adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. - promoter 5' end coordinate + + Coordinate of the 5' end of the promoter within the submitted sequence. + DPBO + DPBO:0000079 + adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. + promoter 5' end coordinate - + - - Coordinate of the 3' end of the promoter within the submitted sequence. - DPBO - DPBO:0000080 - adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. - promoter 3' end coordinate + + Coordinate of the 3' end of the promoter within the submitted sequence. + DPBO + DPBO:0000080 + adapted from the ENA (European Nucleotide Archive) gene promoter template for annotated sequences. + promoter 3' end coordinate - + - - Settings of the gradient used during (e.g. liquid, gas or ion) chromatography - DPBO - DPBO:0000081 - chromatography gradient + + Settings of the gradient used during (e.g. liquid, gas or ion) chromatography + DPBO + DPBO:0000081 + chromatography gradient - + - - Method used for rRNA depletion during construction of the sequencing library. - DPBO - DPBO:0000082 - "see also http://purl.obolibrary.org/obo/NCIT_C18685" - rRNA depletion + + Method used for rRNA depletion during construction of the sequencing library. + DPBO + DPBO:0000082 + "see also http://purl.obolibrary.org/obo/NCIT_C18685" + rRNA depletion - + - - + + - Relative centrifugal force (RCF) is the amount of force applied to a sample when using a centrifuge. It is dependant on the speed of the centrifuge rotation as well as the distance of the sample from the center of rotation. - RCF - DPBO - DPBO:0000083 + Relative centrifugal force (RCF) is the amount of force applied to a sample when using a centrifuge. It is dependant on the speed of the centrifuge rotation as well as the distance of the sample from the center of rotation. + RCF + DPBO + DPBO:0000083 - relative centrifugal force + relative centrifugal force - + - + - G-force is the force acting on an object as a result of acceleration or gravity. - DPBO - DPBO:0000084 - g-force + G-force is the force acting on an object as a result of acceleration or gravity. + DPBO + DPBO:0000084 + g-force - + - + - The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2. - g0 - standard acceleration due to gravity - standard acceleration of free fall - DPBO - DPBO:0000085 - standard gravity + The standard acceleration of an object in free fall at or near sea level equivalent to 9.807 m/s2. + g0 + standard acceleration due to gravity + standard acceleration of free fall + DPBO + DPBO:0000085 + standard gravity - + - - - A library layout which describes that only one end of the library fragment is sequenced - GEO_RNASEQ - RAW FILES_single or paired-end - DPBO - DPBO:0000086 - "Adapted from http://purl.obolibrary.org/obo/FBcv_0003220" - single-end + + + A library layout which describes that only one end of the library fragment is sequenced + GEO_RNASEQ + RAW FILES_single or paired-end + DPBO + DPBO:0000086 + "Adapted from http://purl.obolibrary.org/obo/FBcv_0003220" + single-end - + - - Short unique identifier for the sequencing library - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:0000087 - "Required for upload of next-generation sequencing data to SRA." - library ID + + Short unique identifier for the sequencing library + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:0000087 + "Required for upload of next-generation sequencing data to SRA." + library ID - + - + - A climatic chamber used for growing plants under controlled environmental conditions. - DPBO - DPBO:0000088 - growth chamber + A climatic chamber used for growing plants under controlled environmental conditions. + DPBO + DPBO:0000088 + growth chamber - + - - - Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. - DPBO - DPBO:0000089 - SingleCellExperiment + + + Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries. + DPBO + DPBO:0000089 + SingleCellExperiment - + - - - The core tidyverse includes the packages that you’re likely to use in everyday data analyses. As of tidyverse 1.3.0, the following packages are included in the core tidyverse: ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats. - DPBO - DPBO:0000090 - tidyverse + + + The core tidyverse includes the packages that you’re likely to use in everyday data analyses. As of tidyverse 1.3.0, the following packages are included in the core tidyverse: ggplot2, dplyr, tidyr, readr, purrr, tibble, stringr, forcats. + DPBO + DPBO:0000090 + tidyverse - + - - - A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries. - DPBO - DPBO:0000091 - Matrix + + + A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries. + DPBO + DPBO:0000091 + Matrix - + - - - Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. - DPBO - DPBO:0000092 - scales + + + Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends. + DPBO + DPBO:0000092 + scales - + - - - Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization. - DPBO - DPBO:0000093 - cowplot + + + Provides various features that help with creating publication-quality figures with 'ggplot2', such as a set of themes, functions to align plots and arrange them into complex compound figures, and functions that make it easy to annotate plots and or mix plots with images. The package was originally written for internal use in the Wilke lab, hence the name (Claus O. Wilke's plot package). It has also been used extensively in the book Fundamentals of Data Visualization. + DPBO + DPBO:0000093 + cowplot - + - - - A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc. - DPBO - DPBO:0000094 - RCurl + + + A wrapper for 'libcurl' <https://curl.se/libcurl/> Provides functions to allow one to compose general HTTP requests and provides convenient functions to fetch URIs, get & post forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc. + DPBO + DPBO:0000094 + RCurl - + - - Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality. - DPBO - DPBO:0000095 - R package + + Packages are collections of R functions, data, and compiled code in a well-defined format, created to add specific functionality. + DPBO + DPBO:0000095 + R package - + - - The version of the software package or library that was used in the analysis. - DPBO - DPBO:0000096 - package version + + The version of the software package or library that was used in the analysis. + DPBO + DPBO:0000096 + package version - + - - Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF). - DPBO - DPBO:0000097 - Bruker Corporation term. Definition from https://www.bruker.com/ - prm-PASEF + + Targeted proteomics method that combines parallel reaction monitoring (PRM) and parallel accumulation-serial fragmentation (PASEF). + DPBO + DPBO:0000097 + Bruker Corporation term. Definition from https://www.bruker.com/ + prm-PASEF - + - - Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis. - DPBO - DPBO:0000098 - Bruker Corporation term. Definition from https://www.bruker.com/ - dda-PASEF + + Data-dependent acquisition (DDA) method that uses parallel accumulation-serial fragmentation (PASEF) technology for proteomics analysis. + DPBO + DPBO:0000098 + Bruker Corporation term. Definition from https://www.bruker.com/ + dda-PASEF - + - - Concentration of an antibiotic that was added to a growth medium. - DPBO - DPBO:0000099 - antibiotic concentration + + Concentration of an antibiotic that was added to a growth medium. + DPBO + DPBO:0000099 + antibiotic concentration - + - - Duration of a bacterial cultivation. - DPBO - DPBO:0000100 - growth time + + Duration of a bacterial cultivation. + DPBO + DPBO:0000100 + growth time - + - - The OD600 that was used to inoculate a bacterial culture. - DPBO - DPBO:0000101 - start OD600 + + The OD600 that was used to inoculate a bacterial culture. + DPBO + DPBO:0000101 + start OD600 - + - - Method that was used to harvest bacterial cells. - DPBO - DPBO:0000102 - harvesting method + + Method that was used to harvest bacterial cells. + DPBO + DPBO:0000102 + harvesting method - + - - Constant percentage of dissolved oxygen in a culture medium. - DPBO - DPBO:0000103 - dissolved oxygen (DO) + + Constant percentage of dissolved oxygen in a culture medium. + DPBO + DPBO:0000103 + dissolved oxygen (DO) - + - + - An experiment that is used to grow bacterial cells under oxygen limitation conditions. - DPBO - DPBO:0000104 - oxygen limitation experiment + An experiment that is used to grow bacterial cells under oxygen limitation conditions. + DPBO + DPBO:0000104 + oxygen limitation experiment - + - - Percent of oxygen that is added to a culture medium via gassing. - DPBO - DPBO:0000105 - oxygen concentration + + Percent of oxygen that is added to a culture medium via gassing. + DPBO + DPBO:0000105 + oxygen concentration - + - - Percent of nitrogen that is added to a culture medium via gassing. - DPBO - DPBO:0000106 - nitrogen concentration + + Percent of nitrogen that is added to a culture medium via gassing. + DPBO + DPBO:0000106 + nitrogen concentration - + - + - An experiment that is used to grow bacterial cells under oxygen excess conditions. - DPBO - DPBO:0000107 - oxygen excess experiment + An experiment that is used to grow bacterial cells under oxygen excess conditions. + DPBO + DPBO:0000107 + oxygen excess experiment - + - - A measurement that is used to identify transcriptional binding sites in a genome. - DPBO - DPBO:0000108 - transcriptional binding site identification + + A measurement that is used to identify transcriptional binding sites in a genome. + DPBO + DPBO:0000108 + transcriptional binding site identification - + - - Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata. - Stella Eggels - DPBO - DPBO:0000109 - leaf gas exchange + + Exchange of carbon dioxide, oxygen and water vapor between the plant leaf and the ambient air through stomata. + Stella Eggels + DPBO + DPBO:0000109 + leaf gas exchange - + - - Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation. - Stella Eggels - DPBO - DPBO:0000110 - infrared gas analyzer + + Analyzer that measures the concentration of gases in air based on their absorption of infrared radiation. + Stella Eggels + DPBO + DPBO:0000110 + infrared gas analyzer - + - - A word, term or short statement that clarifies the cause, context and/or consequence of another entity. - DPBO - DPBO:0000111 - Explication + + A word, term or short statement that clarifies the cause, context and/or consequence of another entity. + DPBO + DPBO:0000111 + Explication - + - - Multicellular structure comprising similar cells with some specific function. - DPBO - DPBO:0000112 - adapted from FBcv:0003046 - Tissue + + Multicellular structure comprising similar cells with some specific function. + DPBO + DPBO:0000112 + adapted from FBcv:0003046 + Tissue - + - - The vertical distance below local surface at which the sample was taken. For sediment or soil samples depth is measured from sediment or soil surface, respectively. - DPBO - DPBO:0000113 - adapted from MIXS:0000018 - Sampling depth + + The vertical distance below local surface at which the sample was taken. For sediment or soil samples depth is measured from sediment or soil surface, respectively. + DPBO + DPBO:0000113 + adapted from MIXS:0000018 + Sampling depth - + - - Number of injections of a sample into a mass spectrometer or chromatograph. - DPBO - DPBO:0000114 - Number of injections + + Number of injections of a sample into a mass spectrometer or chromatograph. + DPBO + DPBO:0000114 + Number of injections - + - - Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. - ENVO:01000813 - DPBO - DPBO:00002008 - EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] - environment (feature) + + Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. + ENVO:01000813 + DPBO + DPBO:00002008 + EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] + environment (feature) - + - - Unique identificator for a study. This is used to link experiments to the study. - DPBO - DPBO:0002000 - alias + + Unique identificator for a study. This is used to link experiments to the study. + DPBO + DPBO:0002000 + alias - + - - Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication. - DPBO - DPBO:0002001 - study abstract + + Briefly describes the goals, purpose, and scope of the Study. This need not be listed if it can be inherited from a referenced publication. + DPBO + DPBO:0002001 + study abstract - + - - Title of the study as would be used in a publication. - DPBO - DPBO:0002002 - title + + Title of the study as would be used in a publication. + DPBO + DPBO:0002002 + title - + - - Name of the project within which the experiment was organized. - DPBO - DPBO:0002005 - project name + + Name of the project within which the experiment was organized. + DPBO + DPBO:0002005 + project name - + - - Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid. - DPBO - DPBO:0002006 - sequencing method + + Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid. + DPBO + DPBO:0002006 + sequencing method - + - - Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium - DPBO - DPBO:0002007 - investigation type + + Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardized by Genomic Standards Consortium + DPBO + DPBO:0002007 + investigation type - + - - The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. - ENVO:00010483 - DPBO - DPBO:0002009 - EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] - environment (material) + + The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. + ENVO:00010483 + DPBO + DPBO:0002009 + EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO" [] + environment (material) - + - - MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported - DPBO - DPBO:0002010 - plant-associated environmental package + + MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported + DPBO + DPBO:0002010 + plant-associated environmental package - + - - - The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. + + + The European Nucleotide Archive (ENA) is an open, supported platform for the management, sharing, integration, archiving and dissemination of sequence data. 2022-02-02T08:33:08Z - Dominik Brilhaus - ENSGLOSSARY:0000217 - DPBO - DPBO:0010000 - https://www.ebi.ac.uk/ena/ - ENA + Dominik Brilhaus + ENSGLOSSARY:0000217 + DPBO + DPBO:0010000 + https://www.ebi.ac.uk/ena/ + ENA - + - - - The BioSample database contains descriptions of biological source materials used in experimental assays. + + + The BioSample database contains descriptions of biological source materials used in experimental assays. 2022-02-02T08:33:08Z - Dominik Brilhaus - DPBO - DPBO:0010002 - https://www.ncbi.nlm.nih.gov/biosample/ - BioSample + Dominik Brilhaus + DPBO + DPBO:0010002 + https://www.ncbi.nlm.nih.gov/biosample/ + BioSample - + - - - A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. + + + A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. 2022-02-02T08:58:37Z - Dominik Brilhaus - GENEPIO:0001836 - DPBO - DPBO:0010004 - https://www.ncbi.nlm.nih.gov/bioproject/ - BioProject + Dominik Brilhaus + GENEPIO:0001836 + DPBO + DPBO:0010004 + https://www.ncbi.nlm.nih.gov/bioproject/ + BioProject - + - - - GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis. + + + GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan;41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis. 2022-02-02T08:59:49Z - Dominik Brilhaus - NCIT:C43818 - DPBO - DPBO:0010005 - https://www.ncbi.nlm.nih.gov/genbank/ - GenBank + Dominik Brilhaus + NCIT:C43818 + DPBO + DPBO:0010005 + https://www.ncbi.nlm.nih.gov/genbank/ + GenBank - + - - - Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. + + + Sequence Read Archive (SRA) data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys. SRA stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. 2022-02-02T09:02:27Z - Dominik Brilhaus - DPBO - DPBO:0010006 - https://www.ncbi.nlm.nih.gov/sra/ - SRA + Dominik Brilhaus + DPBO + DPBO:0010006 + https://www.ncbi.nlm.nih.gov/sra/ + SRA - + - - - Plant Genomics & Phenomics Research Data Repository + + + Plant Genomics & Phenomics Research Data Repository 2022-02-02T09:03:35Z - Dominik Brilhaus - DPBO - DPBO:0010007 - https://edal-pgp.ipk-gatersleben.de - PGP + Dominik Brilhaus + DPBO + DPBO:0010007 + https://edal-pgp.ipk-gatersleben.de + PGP - + - - - The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR. + + + The BioImage Archive (BIA) stores and distributes biological images that are useful to life sciences researchers. It also provides data archiving services to the broader bioimaging database community including added-value bioimaging data resources such as EMPIAR, Cell-IDR and Tissue-IDR. 2022-02-02T09:04:46Z - Dominik Brilhaus - DPBO - DPBO:0010008 - https://www.ebi.ac.uk/bioimage-archive/ - BIA + Dominik Brilhaus + DPBO + DPBO:0010008 + https://www.ebi.ac.uk/bioimage-archive/ + BIA - + - - The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay. + + The state (typically fresh or dry) of the biosource material (e.g. tissue) prepared for an assay. - Dominik Brilhaus - DPBO - DPBO:0010009 - "Relates to DPBO:0000013" - biosource material state + Dominik Brilhaus + DPBO + DPBO:0010009 + "Relates to DPBO:0000013" + biosource material state - + - - - Fresh (non-dry) biosource material + + + Fresh (non-dry) biosource material - Dominik Brilhaus - DPBO - DPBO:0010010 - "Relates to https://cropontology.org/rdf/CO_347:0000193 - fresh material + Dominik Brilhaus + DPBO + DPBO:0010010 + "Relates to https://cropontology.org/rdf/CO_347:0000193 + fresh material - + - - - Dry biosource material + + + Dry biosource material - Dominik Brilhaus - DPBO - DPBO:0010011 - "Relates to https://cropontology.org/rdf/CO_347:0000196 - dry material + Dominik Brilhaus + DPBO + DPBO:0010011 + "Relates to https://cropontology.org/rdf/CO_347:0000196 + dry material - + - - Internal standard added in known amount to an analytical sample + + Internal standard added in known amount to an analytical sample - Dominik Brilhaus - DPBO - DPBO:0010012 - "Similar to http://purl.obolibrary.org/obo/MSIO_0000005 - internal standard + Dominik Brilhaus + DPBO + DPBO:0010012 + "Similar to http://purl.obolibrary.org/obo/MSIO_0000005 + internal standard - + - - Volume taken from the sample to be assayed (measured). + + Volume taken from the sample to be assayed (measured). - Dominik Brilhaus - DPBO - DPBO:0010013 - sample volume + Dominik Brilhaus + DPBO + DPBO:0010013 + sample volume - + - - Volume of the sample injected during chromatography + + Volume of the sample injected during chromatography - Dominik Brilhaus - DPBO - DPBO:0010014 - "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577 - chromatography injection volume + Dominik Brilhaus + DPBO + DPBO:0010014 + "Relates to http://purl.allotrope.org/ontologies/result#AFR_0001577 + chromatography injection volume - + - - This is to specify split / splitless runs during e.g. gas-chromatography. + + This is to specify split / splitless runs during e.g. gas-chromatography. - Dominik Brilhaus - DPBO - DPBO:0010015 - "Compare to http://purl.obolibrary.org/obo/OBI_0000525 - chromatography injection mode + Dominik Brilhaus + DPBO + DPBO:0010015 + "Compare to http://purl.obolibrary.org/obo/OBI_0000525 + chromatography injection mode - + - - - placeholder def of RNA-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000003 - To be transformed to an instance. DB - obsolete_RNA-seq + + + placeholder def of RNA-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000003 + To be transformed to an instance. DB + obsolete_RNA-seq true - + - + - A library strategy that can identify and quantify the microRNA sequences present in a biological sample. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000004 - "Adapted from http://purl.obolibrary.org/obo/NCIT_C156057" - miRNA-seq + A library strategy that can identify and quantify the microRNA sequences present in a biological sample. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000004 + "Adapted from http://purl.obolibrary.org/obo/NCIT_C156057" + miRNA-seq - + - + - A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000005 - "Adapted from http://purl.obolibrary.org/obo/NCIT_C172858" - ncRNA-seq + A next-generation sequencing library strategy that can determine the small and large non-protein coding RNA transcripts in a sample. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000005 + "Adapted from http://purl.obolibrary.org/obo/NCIT_C172858" + ncRNA-seq - + - + - A library strategy with an additional size fractionation step after RNA-seq library preparation - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000006 + A library strategy with an additional size fractionation step after RNA-seq library preparation + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000006 - RNA-seq (size fractionation) + RNA-seq (size fractionation) - + - + - A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000007 - "Adapted from http://purl.obolibrary.org/obo/FBcv_0003051" - RNA-seq (CAGE) + A library strategy that is used to sequence the 5' capped transcripts, using CAGE to biotinylate and isolate the 7-methylguanosine cap. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000007 + "Adapted from http://purl.obolibrary.org/obo/FBcv_0003051" + RNA-seq (CAGE) - + - + - Rapid Amplification of cDNA Ends (RACE) is a library strategy for RNA-seq that is used to obtain the full length sequence of an RNA transcript found within a cell. RACE produces a cDNA copy of the RNA through reverse transcription which is amplified and sequenced. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000008 - "Adapted from http://www.ebi.ac.uk/efo/EFO_0004182." - RNA-seq (RACE) + Rapid Amplification of cDNA Ends (RACE) is a library strategy for RNA-seq that is used to obtain the full length sequence of an RNA transcript found within a cell. RACE produces a cDNA copy of the RNA through reverse transcription which is amplified and sequenced. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000008 + "Adapted from http://www.ebi.ac.uk/efo/EFO_0004182." + RNA-seq (RACE) - + - - - placeholder def of ssRNA-seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000009 - To be transformed to an instance. DB - obsolete_ssRNA-seq + + + placeholder def of ssRNA-seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000009 + To be transformed to an instance. DB + obsolete_ssRNA-seq true - + - - - placeholder def of ChIP-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000010 - To be transformed to an instance. DB - obsolete_ChIP-seq + + + placeholder def of ChIP-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000010 + To be transformed to an instance. DB + obsolete_ChIP-seq true - + - - - placeholder def of MNase-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000011 - To be transformed to an instance. DB - obsolete_MNase-seq + + + placeholder def of MNase-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000011 + To be transformed to an instance. DB + obsolete_MNase-seq true - + - - - placeholder def of MBD-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000012 - To be transformed to an instance. DB - obsolete_MBD-seq + + + placeholder def of MBD-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000012 + To be transformed to an instance. DB + obsolete_MBD-seq true - + - - - placeholder def of MRE-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000013 - To be transformed to an instance. DB - obsolete_MRE-seq + + + placeholder def of MRE-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000013 + To be transformed to an instance. DB + obsolete_MRE-seq true - + - - - placeholder def of Bisulfite-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000014 - Replaced by EFO term Bisulfite-seq (id:0003753) - obsolete_Bisulfite-seq + + + placeholder def of Bisulfite-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000014 + Replaced by EFO term Bisulfite-seq (id:0003753) + obsolete_Bisulfite-seq true - + - + - A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation - GEO_RNASEQ - PROTOCOLS_library strategy - RRBS-Seq - reduced-representation bisulfite sequencing - DPBO - DPBO:1000015 - To be transformed to an instance. DB - Bisulfite-seq (reduced representation) - - - - - - - - - placeholder def of MeDIP-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000016 - To be transformed to an instance. DB - obsolete_MeDIP-seq + A library strategy that uses one or more restriction enzymes on a genomic DNA sample prior to sequencing to produce sequence-specific fragmentation + GEO_RNASEQ + PROTOCOLS_library strategy + RRBS-Seq + reduced-representation bisulfite sequencing + DPBO + DPBO:1000015 + To be transformed to an instance. DB + Bisulfite-seq (reduced representation) + + + + + + + + + placeholder def of MeDIP-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000016 + To be transformed to an instance. DB + obsolete_MeDIP-seq true - + - + - A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000017 - "Adapted from FBcv:0003058." - DNase hypersensitivity + A library strategy that is used to characterize the DNase hypersensitivity of a genome by treatment with DNase before library preparation. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000017 + "Adapted from FBcv:0003058." + DNase hypersensitivity - + - + - A library strategy that is used to sequence transposons. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000018 - "Adapted from http://www.ebi.ac.uk/efo/EFO_0008973." - Tn-seq + A library strategy that is used to sequence transposons. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000018 + "Adapted from http://www.ebi.ac.uk/efo/EFO_0008973." + Tn-seq - + - - - placeholder def of FAIRE-seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000019 - To be transformed to an instance. DB - obsolete_FAIRE-seq + + + placeholder def of FAIRE-seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000019 + To be transformed to an instance. DB + obsolete_FAIRE-seq true - + - + - A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment. - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000020 - "Adapted from http://www.ebi.ac.uk/efo/EFO_0008918." - SELEX + A library strategy for high-througput sequencing that is based on Systematic evolution of ligands by exponential enrichment. + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000020 + "Adapted from http://www.ebi.ac.uk/efo/EFO_0008918." + SELEX - + - - - placeholder def of RIP-Seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000021 - To be transformed to an instance. DB - obsolete_RIP-seq + + + placeholder def of RIP-Seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000021 + To be transformed to an instance. DB + obsolete_RIP-seq true - + - - - placeholder def of ATAC-seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000022 - To be transformed to an instance. DB - obsolete_ATAC-seq + + + placeholder def of ATAC-seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000022 + To be transformed to an instance. DB + obsolete_ATAC-seq true - + - - - placeholder def of ChIA-PET - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000023 - To be transformed to an instance. DB - obsolete_ChIA-PET + + + placeholder def of ChIA-PET + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000023 + To be transformed to an instance. DB + obsolete_ChIA-PET true - + - - - placeholder def of Hi-C - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000024 - To be transformed to an instance. DB - obsolete_Hi-C + + + placeholder def of Hi-C + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000024 + To be transformed to an instance. DB + obsolete_Hi-C true - + - + - Any other possible library strategy that can be used for RNA-seq - GEO_RNASEQ - PROTOCOLS_library strategy - DPBO - DPBO:1000025 - "This is a term that is used to enter a library strategy as free text in the checklist of GEO for the upload of RNA-seq data." - OTHER: specify + Any other possible library strategy that can be used for RNA-seq + GEO_RNASEQ + PROTOCOLS_library strategy + DPBO + DPBO:1000025 + "This is a term that is used to enter a library strategy as free text in the checklist of GEO for the upload of RNA-seq data." + OTHER: specify - + - - - placeholder def of fastq - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000026 - To be transformed to an instance. DB - obsolete_fastq + + + placeholder def of fastq + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000026 + To be transformed to an instance. DB + obsolete_fastq true - + - - - Binary format for storing of sequencing data - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000027 - Adapted from http://purl.obolibrary.org/obo/NGBO_6000021. - bam + + + Binary format for storing of sequencing data + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000027 + Adapted from http://purl.obolibrary.org/obo/NGBO_6000021. + bam - + - - - Illumina´s native QSEQ format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000028 - Illumina_native_qseq + + + Illumina´s native QSEQ format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000028 + Illumina_native_qseq - + - - - Illumina´s native sequencing format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000029 - Illumina_native + + + Illumina´s native sequencing format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000029 + Illumina_native - + - - - SOLID´s native csfasta sequencing format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000030 - SOLiD_native_csfasta + + + SOLID´s native csfasta sequencing format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000030 + SOLiD_native_csfasta - + - - - SOLI´s native quality sequencing format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000031 - SOLiD_native_qual + + + SOLI´s native quality sequencing format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000031 + SOLiD_native_qual - + - - - Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000032 - http://edamontology.org/format_3284 - sff + + + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000032 + http://edamontology.org/format_3284 + sff - + - - - 454 pyrosequencing native sequencing file format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000033 - 454_native_seq + + + 454 pyrosequencing native sequencing file format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000033 + 454_native_seq - + - - - 454 pyrosequencing native quality sequencing file format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000034 - 454_native_qual + + + 454 pyrosequencing native quality sequencing file format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000034 + 454_native_qual - + - - - Helicos native file format - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000035 - Helicos_native + + + Helicos native file format + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000035 + Helicos_native - + - - - Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000036 - http://edamontology.org/format_3017 - srf + + + Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000036 + http://edamontology.org/format_3017 + srf - + - - - PacBio hierarchical, filesystem-like data format that can store metadata in the form of user-defined, named attributes, which are attached to groups and datasets, and representations of images and tables built up using datasets, groups and attributes. - GEO_RNASEQ - RAW FILES_file type - DPBO - DPBO:1000037 - Adapted from http://purl.obolibrary.org/obo/NCIT_C184763 - PacBio_HDF5 + + + PacBio hierarchical, filesystem-like data format that can store metadata in the form of user-defined, named attributes, which are attached to groups and datasets, and representations of images and tables built up using datasets, groups and attributes. + GEO_RNASEQ + RAW FILES_file type + DPBO + DPBO:1000037 + Adapted from http://purl.obolibrary.org/obo/NCIT_C184763 + PacBio_HDF5 - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000038 - term is redundant, use EFO:0004202 or OBI:0002000 instead - obsolete_Illumina Genome Analyzer IIx + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000038 + term is redundant, use EFO:0004202 or OBI:0002000 instead + obsolete_Illumina Genome Analyzer IIx true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000039 - term is redundant, use EFO:0004204 or OBI:0002022 instead - obsolete_Illumina HiSeq 1000 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000039 + term is redundant, use EFO:0004204 or OBI:0002022 instead + obsolete_Illumina HiSeq 1000 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000040 - term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027 - obsolete_Illumina HiSeq 1500 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000040 + term is redundant, use GENEPIO:0100115, OBI:0003386 or EFO:0011027 + obsolete_Illumina HiSeq 1500 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000041 - Term is redundant, please use OBI:0002001 or EFO:0004203 - obsolete_Illumina HiSeq 2000 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000041 + Term is redundant, please use OBI:0002001 or EFO:0004203 + obsolete_Illumina HiSeq 2000 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000042 - Term is redundant, please use OBI:0002002 or EFO:0008565 - obsolete_Illumina HiSeq 2500 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000042 + Term is redundant, please use OBI:0002002 or EFO:0008565 + obsolete_Illumina HiSeq 2500 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000043 - Term is redundant, please use OBI:0002048 or EFO:0008564 - obsolete_Illumina HiSeq 3000 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000043 + Term is redundant, please use OBI:0002048 or EFO:0008564 + obsolete_Illumina HiSeq 3000 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000044 - Term is redundant, please use OBI:0002049 or EFO:0008563 - obsolete_Illumina HiSeq 4000 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000044 + Term is redundant, please use OBI:0002049 or EFO:0008563 + obsolete_Illumina HiSeq 4000 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000045 - Term is redundant, please use EFO:0009173 - obsolete_Illumina NextSeq 500 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000045 + Term is redundant, please use EFO:0009173 + obsolete_Illumina NextSeq 500 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000046 - Term is redundant, please use GENEPIO:0100128 or EFO:0008566 - obsolete_Illumina NextSeq 550 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000046 + Term is redundant, please use GENEPIO:0100128 or EFO:0008566 + obsolete_Illumina NextSeq 550 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000047 - Term is redundant, please use GENEPIO:0100113 or OBI:0002129 - obsolete_Illumina HiSeq X Ten + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000047 + Term is redundant, please use GENEPIO:0100113 or OBI:0002129 + obsolete_Illumina HiSeq X Ten true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000048 - Term is redundant, please use GENEPIO:0100112 - obsolete_Illumina HiSeq X Five + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000048 + Term is redundant, please use GENEPIO:0100112 + obsolete_Illumina HiSeq X Five true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000049 - Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637 - obsolete_Illumina NovaSeq 6000 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000049 + Term is redundant, please use GENEPIO:0100123, OBI:0002630 or EFO:0008637 + obsolete_Illumina NovaSeq 6000 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000050 - Redundant term, please use EFO:0004205 instead - obsolete_Illumina MiSeq + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000050 + Redundant term, please use EFO:0004205 instead + obsolete_Illumina MiSeq true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000051 - Redundant term, please use GENEPIO:0100109 instead - obsolete_Illumina HiScanSQ + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000051 + Redundant term, please use GENEPIO:0100109 instead + obsolete_Illumina HiScanSQ true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000052 - Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead. - obsolete_Illumina MiniSeq + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000052 + Term is redundant, please use GENEPIO:0100124, OBI:0003114 or EFO:0008636 instead. + obsolete_Illumina MiniSeq true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000053 - Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead - obsolete_Illumina iSeq 100 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000053 + Term is redundant, please use GENEPIO:0100121 or EFO:0008635 instead + obsolete_Illumina iSeq 100 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000054 - Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead - obsolete_BGISEQ-500 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000054 + Term is redundant, please use NCIT:C146812 or GENEPIO:0100145 instead + obsolete_BGISEQ-500 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000055 - Term is redundant, please use GENEPIO:0100148 - obsolete_DNBSEQ-G400 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000055 + Term is redundant, please use GENEPIO:0100148 + obsolete_DNBSEQ-G400 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000056 - Term is redundant, please use GENEPIO:0100147 - obsolete_DNBSEQ-T7 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000056 + Term is redundant, please use GENEPIO:0100147 + obsolete_DNBSEQ-T7 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000057 - Term is redundant, please use GENEPIO:0100150 - obsolete_DNBSEQ-G50 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000057 + Term is redundant, please use GENEPIO:0100150 + obsolete_DNBSEQ-G50 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000058 - Term is redundant, please use GENEPIO:0100136 - obsolete_Ion Torrent PGM + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000058 + Term is redundant, please use GENEPIO:0100136 + obsolete_Ion Torrent PGM true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000059 - Term is redundant, please use GENEPIO:0100137 - obsolete_Ion Torrent Proton + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000059 + Term is redundant, please use GENEPIO:0100137 + obsolete_Ion Torrent Proton true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000060 - Term is redundant, please use GENEPIO:0100139 - obsolete_Ion Torrent S5 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000060 + Term is redundant, please use GENEPIO:0100139 + obsolete_Ion Torrent S5 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000061 - Term is redundant, please use GENEPIO:0100138 - obsolete_Ion Torrent S5 XL + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000061 + Term is redundant, please use GENEPIO:0100138 + obsolete_Ion Torrent S5 XL true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000062 - Term is redundant, please use GENEPIO:0100131 - obsolete_PacBio RS + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000062 + Term is redundant, please use GENEPIO:0100131 + obsolete_PacBio RS true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000063 - Term is redundant, please use OBI:0002012 or EFO:0008631 - obsolete_PacBio RS II + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000063 + Term is redundant, please use OBI:0002012 or EFO:0008631 + obsolete_PacBio RS II true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000064 - Term is redundant, please use GENEPIO:0100133 or OBI:0002632 - obsolete_Sequel + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000064 + Term is redundant, please use GENEPIO:0100133 or OBI:0002632 + obsolete_Sequel true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000065 - Term is redundant, please use GENEPIO:0100134 or OBI:0002633 - obsolete_Sequel II + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000065 + Term is redundant, please use GENEPIO:0100134 or OBI:0002633 + obsolete_Sequel II true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000066 - Term is redundant, please use GENEPIO:0001932 or EFO:0004442 - obsolete_AB SOLiD System 2.0 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000066 + Term is redundant, please use GENEPIO:0001932 or EFO:0004442 + obsolete_AB SOLiD System 2.0 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000067 - Term is redundant, please use EFO:0004439 or GENEPIO:0001933 - obsolete_AB SOLiD System 3.0 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000067 + Term is redundant, please use EFO:0004439 or GENEPIO:0001933 + obsolete_AB SOLiD System 3.0 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000068 - Term is redundant, please use OBI:0002007. - obsolete_AB SOLiD 3 Plus System + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000068 + Term is redundant, please use OBI:0002007. + obsolete_AB SOLiD 3 Plus System true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000069 - Term is redundant, please use EFO:0004438 - obsolete_AB SOLiD 4 System + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000069 + Term is redundant, please use EFO:0004438 + obsolete_AB SOLiD 4 System true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000070 - Term is redundant, please use GENEPIO:0001928 or EFO:0004441 - obsolete_AB SOLiD 4hq System + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000070 + Term is redundant, please use GENEPIO:0001928 or EFO:0004441 + obsolete_AB SOLiD 4hq System true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000071 - Term is redundant, please use EFO:0004437 or GENEPIO:0001931 - obsolete_AB SOLiD PI System + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000071 + Term is redundant, please use EFO:0004437 or GENEPIO:0001931 + obsolete_AB SOLiD PI System true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000072 - AB 5500 Genetic Analyzer + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000072 + AB 5500 Genetic Analyzer - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000073 - AB 5500xl Genetic Analyzer + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000073 + AB 5500xl Genetic Analyzer - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000074 - AB 5500xl-W Genetic Analysis System + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000074 + AB 5500xl-W Genetic Analysis System - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000075 - Term is redundant, please use EFO:0004431 - obsolete_454 GS + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000075 + Term is redundant, please use EFO:0004431 + obsolete_454 GS true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000076 - Term is redundant, please use EFO:0004206 - obsolete_454 GS 20 + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000076 + Term is redundant, please use EFO:0004206 + obsolete_454 GS 20 true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000077 - Term is redundant, please use EFO:0004432 or OBI:0000702 - obsolete_454 GS FLX + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000077 + Term is redundant, please use EFO:0004432 or OBI:0000702 + obsolete_454 GS FLX true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000078 - 454 GS FLX+ + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000078 + 454 GS FLX+ - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000079 - Term is redundant, please use EFO:0004434 or GENEPIO:0001938 - obsolete_454 GS Junior + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000079 + Term is redundant, please use EFO:0004434 or GENEPIO:0001938 + obsolete_454 GS Junior true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000080 - Term is redundant, please use EFO:0004433 or GENEPIO:0001936 - obsolete_454 GS FLX Titanium + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000080 + Term is redundant, please use EFO:0004433 or GENEPIO:0001936 + obsolete_454 GS FLX Titanium true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000081 - Term is redundant, please use NCIT:C146815 or GENEPIO:0001924 - obsolete_Complete Genomics + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000081 + Term is redundant, please use NCIT:C146815 or GENEPIO:0001924 + obsolete_Complete Genomics true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000082 - Term is redundant, please use OBI:0000717 - obsolete_Helicos HeliScope + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000082 + Term is redundant, please use OBI:0000717 + obsolete_Helicos HeliScope true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000083 - Term is redundant, please use GENEPIO:0100141 - obsolete_GridION + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000083 + Term is redundant, please use GENEPIO:0100141 + obsolete_GridION true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000084 - Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142 - obsolete_MinION + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000084 + Term is redundant, please use OBI:0002750, EFO:0008632 or GENEPIO:0100142 + obsolete_MinION true - + - - - GEO_RNASEQ - RAW FILES_instrument model - DPBO - DPBO:1000085 - Term is redundant, please use OBI:0002752 or GENEPIO:0100143 - obsolete_PromethION + + + GEO_RNASEQ + RAW FILES_instrument model + DPBO + DPBO:1000085 + Term is redundant, please use OBI:0002752 or GENEPIO:0100143 + obsolete_PromethION true - + - - - placeholder def of single - GEO_RNASEQ - RAW FILES_single or paired-end - DPBO - DPBO:1000086 - Deprecated, please use DPBO:0000086 "single-end" instead - obsolete_single + + + placeholder def of single + GEO_RNASEQ + RAW FILES_single or paired-end + DPBO + DPBO:1000086 + Deprecated, please use DPBO:0000086 "single-end" instead + obsolete_single true - + - - - A library layout which describes that both ends of the library fragment are sequenced - GEO_RNASEQ - RAW FILES_single or paired-end - DPBO - DPBO:1000087 - Adapted from http://purl.obolibrary.org/obo/FBcv_0003221 - paired-end + + + A library layout which describes that both ends of the library fragment are sequenced + GEO_RNASEQ + RAW FILES_single or paired-end + DPBO + DPBO:1000087 + Adapted from http://purl.obolibrary.org/obo/FBcv_0003221 + paired-end - + - - - placeholder def of total RNA - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000088 - term is redundant, please use EFO:0004964 - obsolete_total RNA + + + placeholder def of total RNA + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000088 + term is redundant, please use EFO:0004964 + obsolete_total RNA true - + - - - placeholder def of polyA RNA - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000089 - Term is redundant, please use OBI_0000869 - obsolete_polyA RNA + + + placeholder def of polyA RNA + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000089 + Term is redundant, please use OBI_0000869 + obsolete_polyA RNA - + - - - placeholder def of cytoplasmic RNA - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000090 - Term is redundant, please use NCIT:C84512 - obsolete_cytoplasmic RNA + + + placeholder def of cytoplasmic RNA + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000090 + Term is redundant, please use NCIT:C84512 + obsolete_cytoplasmic RNA true - + - - - placeholder def of nuclear RNA - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000091 - Term is redundant. Please use EFO:0030052 - obsolete_nuclear RNA + + + placeholder def of nuclear RNA + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000091 + Term is redundant. Please use EFO:0030052 + obsolete_nuclear RNA true - + - - - placeholder def of genomic DNA - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000092 - Term is redundant, please use BAO:0000316 - obsolete_genomic DNA + + + placeholder def of genomic DNA + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000092 + Term is redundant, please use BAO:0000316 + obsolete_genomic DNA true - + - - - placeholder def of protein - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000093 - Term is redundant, please use CHEBI:36080 - obsolete_protein + + + placeholder def of protein + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000093 + Term is redundant, please use CHEBI:36080 + obsolete_protein true - + - - - Any other bio entity that can be characterized by high-throuput sequencing. - GEO_RNASEQ - SAMPLES_molecule - DPBO - DPBO:1000094 - other + + + Any other bio entity that can be characterized by high-throuput sequencing. + GEO_RNASEQ + SAMPLES_molecule + DPBO + DPBO:1000094 + other - + - - Parent term to collect endpoint repositories (ER). - DPBO - DPBO:1000095 - "For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org" - endpoint repository + + Parent term to collect endpoint repositories (ER). + DPBO + DPBO:1000095 + "For an overview of relevant repositories, check https://www.re3data.org or https://fairsharing.org" + endpoint repository - + - - - - GEO (Gene Expression Omnibus) is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. - DPBO - DPBO:1000096 - https://www.ncbi.nlm.nih.gov/geo/ - GEO + + + + GEO (Gene Expression Omnibus) is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. + DPBO + DPBO:1000096 + https://www.ncbi.nlm.nih.gov/geo/ + GEO - + - - - MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals. - DPBO - DPBO:1000097 - https://www.ebi.ac.uk/metabolights/ - MetaboLights + + + MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. MetaboLights is the recommended Metabolomics repository for a number of leading journals. + DPBO + DPBO:1000097 + https://www.ebi.ac.uk/metabolights/ + MetaboLights - + - - - The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets. - DPBO - DPBO:1000098 - https://www.ebi.ac.uk/pride/ - PRIDE + + + The PRIDE PRoteomics IDEntifications (PRIDE) Archive database is a centralized, standards compliant, public data repository for mass spectrometry proteomics data, including protein and peptide identifications and the corresponding expression values, post-translational modifications and supporting mass spectra evidence (both as raw data and peak list files). PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a standardised way for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to ProteomeXchange via PRIDE and are handled by expert bio-curators. All PRIDE public datasets can also be searched in ProteomeCentral, the portal for all ProteomeXchange datasets. + DPBO + DPBO:1000098 + https://www.ebi.ac.uk/pride/ + PRIDE - + - - - - Parent term to collect terms required for RNASeq submission to GEO - DPBO - DPBO:1000099 - GEO_RNAseq + + + + Parent term to collect terms required for RNASeq submission to GEO + DPBO + DPBO:1000099 + GEO_RNAseq - + - - - Parent term to collect terms required for microarray submission to GEO - DPBO - DPBO:1000100 - GEO_microarray + + + Parent term to collect terms required for microarray submission to GEO + DPBO + DPBO:1000100 + GEO_microarray - + - - - A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. - OME:Well - DPBO - DPBO:1000101 - term is redundant, please use REPR:Well - obsolete_well + + + A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. + OME:Well + DPBO + DPBO:1000101 + term is redundant, please use REPR:Well + obsolete_well true - + - - The number of a well in a well plate. - DPBO - DPBO:1000102 - well Number + + The number of a well in a well plate. + DPBO + DPBO:1000102 + well Number - + - - The identifier of a siRNA from a reagent library. - DPBO - DPBO:1000103 - siRNA identifier + + The identifier of a siRNA from a reagent library. + DPBO + DPBO:1000103 + siRNA identifier - + - - - Unique name of a chemical compound. - EDAM:data_0990 - DPBO - DPBO:1000104 - term is redundant, please use data:0990 - obsolete_compound name + + + Unique name of a chemical compound. + EDAM:data_0990 + DPBO + DPBO:1000104 + term is redundant, please use data:0990 + obsolete_compound name true - + - - - Identifier of an entry from a database of chemicals. - data:1086 - DPBO - DPBO:1000105 - term is redundant, please use data:1086 - obsolete_compound identifier + + + Identifier of an entry from a database of chemicals. + data:1086 + DPBO + DPBO:1000105 + term is redundant, please use data:1086 + obsolete_compound identifier true - + - - The class a compound belongs to, defined by its biological function or the chemical property. - DPBO - DPBO:1000106 - "Needed for imaging templates" - compound class + + The class a compound belongs to, defined by its biological function or the chemical property. + DPBO + DPBO:1000106 + "Needed for imaging templates" + compound class - + - - - A unique gene name within a specific repository, database, or collection. - NCIT:C48664 - DPBO - DPBO:1000108 - obsolete_gene identifier + + + A unique gene name within a specific repository, database, or collection. + NCIT:C48664 + DPBO + DPBO:1000108 + obsolete_gene identifier true - + - - The sequence of the sense strand. - DPBO - DPBO:1000109 - "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" - sense sequence + + The sequence of the sense strand. + DPBO + DPBO:1000109 + "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" + sense sequence - + - - The sequence of the antisense strand. - DPBO - DPBO:1000110 - "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" - antisense sequence + + The sequence of the antisense strand. + DPBO + DPBO:1000110 + "definition from BIA idr0000-screenA-library.xlxs from: https://idr.openmicroscopy.org/about/submission.html" + antisense sequence - + - - - A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated. - NCIT:C49647 - DPBO - DPBO:1000111 - term is redundant, please use NCIT:C49647 - obsolete_control type + + + A characteristic of a treatment regimen employed as a comparator against which the study treatment is evaluated. + NCIT:C49647 + DPBO + DPBO:1000111 + term is redundant, please use NCIT:C49647 + obsolete_control type true - + - - Result of quality control. This can be: pass/fail, or other information such as: no cells - DPBO - DPBO:1000112 - "Definition according to IDR" - quality control + + Result of quality control. This can be: pass/fail, or other information such as: no cells + DPBO + DPBO:1000112 + "Definition according to IDR" + quality control - + - - The label used in a microscopy assay and what it targets, separated by a colon. Each pair of labels and visualized object is separated by a semi-colon. E.g. DAPI:nuclei;TRITC:HA_Flag tagged protein. - DPBO - DPBO:1000113 - "Needed for imaging templates. Definition form IDR" - channel + + The label used in a microscopy assay and what it targets, separated by a colon. Each pair of labels and visualized object is separated by a semi-colon. E.g. DAPI:nuclei;TRITC:HA_Flag tagged protein. + DPBO + DPBO:1000113 + "Needed for imaging templates. Definition form IDR" + channel - + - - The type of a high content screening experiment like RNAi screen or antibody screen. - DPBO - DPBO:1000114 - "Needed for imaging templates" - screen technology type + + The type of a high content screening experiment like RNAi screen or antibody screen. + DPBO + DPBO:1000114 + "Needed for imaging templates" + screen technology type - + - - Version of a reagent library used e.g. in high content screening. - DPBO - DPBO:1000116 - "Needed for imaging templates" - library version + + Version of a reagent library used e.g. in high content screening. + DPBO + DPBO:1000116 + "Needed for imaging templates" + library version - + - - - A type of protein made by B lymphocytes in response to a foreign substance (antigen). Each antibody only binds to a specific antigen, helping to destroy the antigen directly or by assisting white blood cells to destroy the antigen. - NCIT:C16295 - DPBO - DPBO:1000117 - term is redundant, please use NCIT:C16295 - obsolete_antibody + + + A type of protein made by B lymphocytes in response to a foreign substance (antigen). Each antibody only binds to a specific antigen, helping to destroy the antigen directly or by assisting white blood cells to destroy the antigen. + NCIT:C16295 + DPBO + DPBO:1000117 + term is redundant, please use NCIT:C16295 + obsolete_antibody true - + - - - A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope. - NCIT:C126370 - DPBO - DPBO:1000118 - use NCIT:C126370 - obsolete_cover slip + + + A thin flat piece of transparent material that is placed over a specimen for viewing with a microscope. + NCIT:C126370 + DPBO + DPBO:1000118 + use NCIT:C126370 + obsolete_cover slip true - + - - DPBO - DPBO:1000120 - "Needed for imaging templates" - image file path + + DPBO + DPBO:1000120 + "Needed for imaging templates" + image file path - + - - Compartment of interest in the prepared sample - DPBO - DPBO:1000121 - "Needed for imaging templates" - target compartment + + Compartment of interest in the prepared sample + DPBO + DPBO:1000121 + "Needed for imaging templates" + target compartment - + - - - The name of the software program to capture and/or process imaging data. - NCIT:C175898 - DPBO - DPBO:1000122 - false - obsolete_imaging software name + + + The name of the software program to capture and/or process imaging data. + NCIT:C175898 + DPBO + DPBO:1000122 + false + obsolete_imaging software name true - + - - The version of the software program to capture and/or process imaging data. - DPBO - DPBO:1000123 - "Needed for imaging templates" - imaging software version + + The version of the software program to capture and/or process imaging data. + DPBO + DPBO:1000123 + "Needed for imaging templates" + imaging software version - + - - The used settings in the software program to capture and/or process imaging data. - DPBO - DPBO:1000124 - "Needed for imaging templates" - imaging software settings + + The used settings in the software program to capture and/or process imaging data. + DPBO + DPBO:1000124 + "Needed for imaging templates" + imaging software settings - + - - Channel the image was taken with. - DPBO - DPBO:1000125 - "Needed for imaging templates" - microscope filter + + Channel the image was taken with. + DPBO + DPBO:1000125 + "Needed for imaging templates" + microscope filter - + - - dwc:datasetName - DPBO - DPBO:1000126 - "Needed for imaging templates" - dataset name + + dwc:datasetName + DPBO + DPBO:1000126 + "Needed for imaging templates" + dataset name - + - - - The name of the assay. - NCIT:C178857 - DPBO - DPBO:1000127 - obsolete_assay name + + + The name of the assay. + NCIT:C178857 + DPBO + DPBO:1000127 + obsolete_assay name true - + - - Software used for the processing of microscopy images like for adaption of contrast or stacking. - DPBO - DPBO:1000128 - "Needed for imaging templates" - image processing software + + Software used for the processing of microscopy images like for adaption of contrast or stacking. + DPBO + DPBO:1000128 + "Needed for imaging templates" + image processing software - + - - Software used to analyze data extracted from microscopy images. - DPBO - DPBO:1000129 - "Needed for imaging templates" - image data analysis software + + Software used to analyze data extracted from microscopy images. + DPBO + DPBO:1000129 + "Needed for imaging templates" + image data analysis software - + - - Applied settings of the software used for the processing of microscopy images - DPBO - DPBO:1000130 - "Needed for imaging templates" - image processing software parameters + + Applied settings of the software used for the processing of microscopy images + DPBO + DPBO:1000130 + "Needed for imaging templates" + image processing software parameters - + - - Software used for the extraction of features from microscopy images. - DPBO - DPBO:1000131 - "Needed for imaging templates" - feature extraction software + + Software used for the extraction of features from microscopy images. + DPBO + DPBO:1000131 + "Needed for imaging templates" + feature extraction software - + - - Description of the approach to extract features from microscopy images. - DPBO - DPBO:1000133 - "Needed for imaging templates" - feature extraction strategy + + Description of the approach to extract features from microscopy images. + DPBO + DPBO:1000133 + "Needed for imaging templates" + feature extraction strategy - + - - Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it. - DPBO - DPBO:1000135 - "Needed for imaging templates" - use of image + + Whether a microscopy image is intended to be used illustrational or analytically by deriving values from it. + DPBO + DPBO:1000135 + "Needed for imaging templates" + use of image - + - - The gene annotation build the siRNAs for a high content screen library were mapped to. - DPBO - DPBO:1000136 - "Needed for imaging templates" - reagent design genome reference version + + The gene annotation build the siRNAs for a high content screen library were mapped to. + DPBO + DPBO:1000136 + "Needed for imaging templates" + reagent design genome reference version - + - - additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype' - DPBO - DPBO:1000137 - "Needed for imaging templates. Definition from IDR." - control specification + + additional information about the quality control in high content screening studies e.g. 'checks for transfection', 'gives strong phenotype' + DPBO + DPBO:1000137 + "Needed for imaging templates. Definition from IDR." + control specification - + - - additional information why a quality control passed or failed' - DPBO - DPBO:1000138 - "Needed for imaging templates. Definition from IDR." - quality control comments + + additional information why a quality control passed or failed' + DPBO + DPBO:1000138 + "Needed for imaging templates. Definition from IDR." + quality control comments - + - - Type of an imaging study. - DPBO - DPBO:1000139 - "Needed for imaging templates" - microscopy study type + + Type of an imaging study. + DPBO + DPBO:1000139 + "Needed for imaging templates" + microscopy study type - + - - The magnification of a microscopy image - DPBO - DPBO:1000140 - "Needed for imaging templates" - magnification + + The magnification of a microscopy image + DPBO + DPBO:1000140 + "Needed for imaging templates" + magnification - + - - The sizes along the axis of the XYZCT dimensions in a microscopy image. - DPBO - DPBO:1000141 - "Needed for imaging templates" - image dimensionality + + The sizes along the axis of the XYZCT dimensions in a microscopy image. + DPBO + DPBO:1000141 + "Needed for imaging templates" + image dimensionality - + - - - The microscope's objective lens. - OME:Objective - DPBO - DPBO:1000142 - use OME:objective - obsolete_objective + + + The microscope's objective lens. + OME:Objective + DPBO + DPBO:1000142 + use OME:objective + obsolete_objective true - + - - How a sample was further prepared for microscopy. - MS:1000831 - DPBO - DPBO:1000143 - microscopy sample preparation + + How a sample was further prepared for microscopy. + MS:1000831 + DPBO + DPBO:1000143 + microscopy sample preparation - + - - Plant material fixation on a microscopy slide. - DPBO - DPBO:1000144 - "Needed for imaging templates" - material fixation + + Plant material fixation on a microscopy slide. + DPBO + DPBO:1000144 + "Needed for imaging templates" + material fixation - + - - The part of an organism that has been prepared for an experiment - DPBO - DPBO:1000145 - "Needed for imaging templates" - prepared organism part + + The part of an organism that has been prepared for an experiment + DPBO + DPBO:1000145 + "Needed for imaging templates" + prepared organism part - + - - - A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. - "Fabian Haas | ORCID:0000-0002-7711-5282" - EFO:0005135 - DPBO - DPBO:1000146 - use EFO:0005135 - obsolete_strain + + + A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. + "Fabian Haas | ORCID:0000-0002-7711-5282" + EFO:0005135 + DPBO + DPBO:1000146 + use EFO:0005135 + obsolete_strain true - + - - - A device that can be used to restrict the location of material entities over time - "Fabian Haas | ORCID:0000-0002-7711-5282" - OBI:0000967 - DPBO - DPBO:1000147 - term is redundant, please use OBI:0000967 - obsolete_container + + + A device that can be used to restrict the location of material entities over time + "Fabian Haas | ORCID:0000-0002-7711-5282" + OBI:0000967 + DPBO + DPBO:1000147 + term is redundant, please use OBI:0000967 + obsolete_container true - + - + - A wide-mouthed cylindrical container made of glass or pottery and typically having a lid - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000148 - jar + A wide-mouthed cylindrical container made of glass or pottery and typically having a lid + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000148 + jar - + - + - A flat dish, typically circular - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000149 - plate + A flat dish, typically circular + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000149 + plate - + - - - The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. [database_cross_reference: https://en.wikipedia.org/wiki/Contamination][database_cross_reference: https://github.com/pato-ontology/pato/issues/420] - "Fabian Haas | ORCID:0000-0002-7711-5282" - PATO:0015031 - DPBO - DPBO:1000150 - obsolete_contamination + + + The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. [database_cross_reference: https://en.wikipedia.org/wiki/Contamination][database_cross_reference: https://github.com/pato-ontology/pato/issues/420] + "Fabian Haas | ORCID:0000-0002-7711-5282" + PATO:0015031 + DPBO + DPBO:1000150 + obsolete_contamination true - + - + - Free from other living organisms - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000151 - axenic + Free from other living organisms + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000151 + axenic - + - + - Latest laboratory cultivated the strain. Who sent the strain to your laboratory - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000152 - laboratory strain + Latest laboratory cultivated the strain. Who sent the strain to your laboratory + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000152 + laboratory strain - + - - The day of the month or year as specified by a number. According to ISO 8601-1 [ISO 8601-1] please use the format YYYY-MM-DD. - "Fabian Haas | ORCID:0000-0002-7711-5282" - dc:date - DPBO - DPBO:1000153 - date + + The day of the month or year as specified by a number. According to ISO 8601-1 [ISO 8601-1] please use the format YYYY-MM-DD. + "Fabian Haas | ORCID:0000-0002-7711-5282" + dc:date + DPBO + DPBO:1000153 + date - + - - - A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. [database_cross_reference: PATOC:GVG] - "Fabian Haas | ORCID:0000-0002-7711-5282" - PATO:0000918 - DPBO - DPBO:1000154 - term is redundant, please use PATO:0000918 - obsolete_volume + + + A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. [database_cross_reference: PATOC:GVG] + "Fabian Haas | ORCID:0000-0002-7711-5282" + PATO:0000918 + DPBO + DPBO:1000154 + term is redundant, please use PATO:0000918 + obsolete_volume true - + - + - Volume of culture medium used to grow the organism - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000155 - culture medium volume + Volume of culture medium used to grow the organism + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000155 + culture medium volume - + - - - The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. - "Fabian Haas | ORCID:0000-0002-7711-5282" - EFO:0000568 - DPBO - DPBO:1000156 - term is redundant, please use EFO:0000568 - obsolete_light + + + The photoperiod and type (e.g., natural, restricted wavelength) of light exposure. + "Fabian Haas | ORCID:0000-0002-7711-5282" + EFO:0000568 + DPBO + DPBO:1000156 + term is redundant, please use EFO:0000568 + obsolete_light true - + - + - The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source) - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000157 - "close to the term http://purl.obolibrary.org/obo/PECO_0007154" - light quality + The spectral distribution of light (blue, green, red, far red and other light spectrums emitted from a light source) + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000157 + "close to the term http://purl.obolibrary.org/obo/PECO_0007154" + light quality - + - - - A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000158 - term is redundant, please use UO:0010006 - obsolete_ratio + + + A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000158 + term is redundant, please use UO:0010006 + obsolete_ratio true - + - A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. - UOB:LKSR + A dimensionless ratio unit which, given a pair of quantities a and b, for which b is a multiple of a, denotes b by giving the multiplier (coefficient) c for a to result in b. + UOB:LKSR - + - + - Nucleic acids have absorbance maxima at 260 nm. Historically, the ratio of this absorbance maximum to the absorbance at 280 nm has been used as a measure of purity in both DNA and RNA extractions. A 260/280 ratio of ~1.8 is generally accepted as pure for DNA; a ratio of ~2.0 is generally accepted as pure for RNA. - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000159 - "Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf" - 260/280 ratio + Nucleic acids have absorbance maxima at 260 nm. Historically, the ratio of this absorbance maximum to the absorbance at 280 nm has been used as a measure of purity in both DNA and RNA extractions. A 260/280 ratio of ~1.8 is generally accepted as pure for DNA; a ratio of ~2.0 is generally accepted as pure for RNA. + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000159 + "Thermofisher NanoDrop https://tools.thermofisher.com/content/sfs/brochures/T123-NanoDrop-Lite-Interpretation-of-Nucleic-Acid-260-280-Ratios.pdf" + 260/280 ratio - + - + - The 260/230 values for pure nucleic acid are often higher than the respective 260/280 values. Expected 260/230 values are commonly in the range of 2.0–2.2 - "Fabian Haas | ORCID:0000-0002-7711-5282" - DPBO - DPBO:1000160 - "Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf" - 260/230 ratio + The 260/230 values for pure nucleic acid are often higher than the respective 260/280 values. Expected 260/230 values are commonly in the range of 2.0–2.2 + "Fabian Haas | ORCID:0000-0002-7711-5282" + DPBO + DPBO:1000160 + "Thermofisher NanoDrop https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf" + 260/230 ratio - + - - ISA-related term to identify the type of protocol (the set of procedures and rules that must be performed and when) used during the study or assay. - Dominik Brilhaus - DPBO - DPBO:1000161 - "This term is primarily used to group and hierarchically categorize types of experimental protocols for easier (interpretation of) user-input. For the initial categorization, 'type' is defined as the purpose of the experiment (i.e. extraction of a target material such as DNA) rather than the mechanism of the protocol (i.e. column-based extraction)." - protocol type + + ISA-related term to identify the type of protocol (the set of procedures and rules that must be performed and when) used during the study or assay. + Dominik Brilhaus + DPBO + DPBO:1000161 + "This term is primarily used to group and hierarchically categorize types of experimental protocols for easier (interpretation of) user-input. For the initial categorization, 'type' is defined as the purpose of the experiment (i.e. extraction of a target material such as DNA) rather than the mechanism of the protocol (i.e. column-based extraction)." + protocol type - + - - - A protocol that provides instructions for the growth of a biological sample. Describes the conditions, materials and procedure used to grow and/or maintain the sample. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - EFO:0003789 - DPBO - DPBO:1000162 - replaced term with EFO:0003789 - obsolete_growth protocol + + + A protocol that provides instructions for the growth of a biological sample. Describes the conditions, materials and procedure used to grow and/or maintain the sample. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + EFO:0003789 + DPBO + DPBO:1000162 + replaced term with EFO:0003789 + obsolete_growth protocol true - + - + - A protocol that provides instructions for growing algae. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000163 - algae growth protocol + A protocol that provides instructions for growing algae. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000163 + algae growth protocol - + - + - A protocol that provides instructions for growing a plant cultivar. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000164 - plant growth protocol + A protocol that provides instructions for growing a plant cultivar. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000164 + plant growth protocol - + - + - A protocol that provides instructions for growing a microbial sample. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000165 - microbe growth protocol + A protocol that provides instructions for growing a microbial sample. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000165 + microbe growth protocol - + - - - A protocol that provides instructions for growing a bacterial sample. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000166 - bacteria growth protocol + + + A protocol that provides instructions for growing a bacterial sample. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000166 + bacteria growth protocol - + - - - A protocol that provides instructions for growing yeast. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000167 - yeast growth protocol + + + A protocol that provides instructions for growing yeast. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000167 + yeast growth protocol - + - - - A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - EFO:0003969 - DPBO - DPBO:1000168 - definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969 - obsolete_treatment protocol + + + A protocol that aims to treat sample or collection of samples, organism or group of organisms, for some experimental purpose. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + EFO:0003969 + DPBO + DPBO:1000168 + definition from http://www.ebi.ac.uk/efo/EFO_0003969. Term is redundant, please use EFO:0003969 + obsolete_treatment protocol true - + - - - A protocol that provides instructions on how a biological sample for an experiment was collected. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - EFO:0005518 - DPBO - DPBO:1000169 - definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518 - obsolete_sample collection protocol + + + A protocol that provides instructions on how a biological sample for an experiment was collected. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + EFO:0005518 + DPBO + DPBO:1000169 + definition from http://www.ebi.ac.uk/efo/EFO_0005518. Term is redundant, please use EFO:0005518 + obsolete_sample collection protocol true - + - - - A protocol that details how a sample is processed or changed to prepare it for analysis. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000170 - sample processing protocol + + + A protocol that details how a sample is processed or changed to prepare it for analysis. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000170 + sample processing protocol - + - - - A protocol used to obtain something of experimental interest from a sample via chemical, physical or mechanical means. Often tailored to match the starting material as well as the end goals (resulting material, quality level, etc.) of the procedure required by the following assay - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - EFO:0000490 - DPBO - DPBO:1000171 - definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490 - obsolete_extraction protocol + + + A protocol used to obtain something of experimental interest from a sample via chemical, physical or mechanical means. Often tailored to match the starting material as well as the end goals (resulting material, quality level, etc.) of the procedure required by the following assay + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + EFO:0000490 + DPBO + DPBO:1000171 + definition taken heavily from http://www.ebi.ac.uk/efo/EFO_0000490. Term is redundant, please use EFO:0000490 + obsolete_extraction protocol true - + - - - A protocol that describes how to remove and purify DNA from a sample. This requires physical and/or chemical methods in order to separate the DNA from cell membranes, proteins and other cellular components. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000172 - definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384. - obsolete_DNA extraction protocol + + + A protocol that describes how to remove and purify DNA from a sample. This requires physical and/or chemical methods in order to separate the DNA from cell membranes, proteins and other cellular components. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000172 + definition taken from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425773/. Term is redundant, please use EFO:0022384. + obsolete_DNA extraction protocol true - + - - - A protocol that describes the steps for removing and purifying DNA from a biological sample - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - EFO:0010959 - DPBO - DPBO:1000173 - term is redundant, please use EFO:0010959 - obsolete_RNA extraction protocol + + + A protocol that describes the steps for removing and purifying DNA from a biological sample + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + EFO:0010959 + DPBO + DPBO:1000173 + term is redundant, please use EFO:0010959 + obsolete_RNA extraction protocol true - + - - - A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000174 - term is redundant, please use EFO:0022383 - obsolete_protein extraction protocol + + + A protocol that describes how to isolate protein from a tissue, cell culture or other biological sample. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000174 + term is redundant, please use EFO:0022383 + obsolete_protein extraction protocol true - + - + - A protocol that describes the step by step process for removing metabolites from a biological sample. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000175 - metabolite extraction protocol + A protocol that describes the step by step process for removing metabolites from a biological sample. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000175 + metabolite extraction protocol - + - - - A protocol that describes the steps to be taken to transform a sample before an assay can be performed - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000176 - assay pre-processing protocol + + + A protocol that describes the steps to be taken to transform a sample before an assay can be performed + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000176 + assay pre-processing protocol - + - - - A protocol that describes how to perform an assay. - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000177 - assay protocol + + + A protocol that describes how to perform an assay. + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000177 + assay protocol - + - - - A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information. - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000178 - definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925 - data processing protocol + + + A protocol that describes the operations performed on data by a computer in order to retrieve, transform, or classify information. + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000178 + definition heavily based on http://purl.obolibrary.org/obo/NCIT_C47925 + data processing protocol - + - - - A protocol that describes the operations performed to filter or select a smaller part of the dataset to be used for or rejected from subsequent analysis steps - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000179 - data filtering protocol + + + A protocol that describes the operations performed to filter or select a smaller part of the dataset to be used for or rejected from subsequent analysis steps + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000179 + data filtering protocol - + - - - A protocol that describes the operations performed to convert data from one format, structure, or value into another. - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000180 - data transformation protocol + + + A protocol that describes the operations performed to convert data from one format, structure, or value into another. + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000180 + data transformation protocol - + - - - A protocol that describes the operations performed to take a specific data set out of a larger data set and present it in a useable format. - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - DPBO - DPBO:1000181 - data extraction protocol + + + A protocol that describes the operations performed to take a specific data set out of a larger data set and present it in a useable format. + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + DPBO + DPBO:1000181 + data extraction protocol - + - - An unique identifier for grouping experminental replicates - replication of an experiment to assess biological or technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, replicate groups must be the same for each replicate in the group (e.g. 'group 1' for each replicate in the group). This adds the possibility to aggregate the replicates without additional annotations. - Kevin Schneider | ORCID: 0000-0002-2198-5262 - DPBO - DPBO:1000182 - replicate group + + An unique identifier for grouping experminental replicates - replication of an experiment to assess biological or technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, replicate groups must be the same for each replicate in the group (e.g. 'group 1' for each replicate in the group). This adds the possibility to aggregate the replicates without additional annotations. + Kevin Schneider | ORCID: 0000-0002-2198-5262 + DPBO + DPBO:1000182 + replicate group - + - - - An unique identifier for grouping biological replicates - replicates made from different individual biosamples to assess biological variation in an experiment. In contrast to other ways of annotating replicates in experimental design, biological replicate groups must be the same for each replicate in the group (e.g. 'b_1' for each biological replicate in the group). This adds the possibility to aggregate the biological replicates without additional annotations. - Kevin Schneider | ORCID: 0000-0002-2198-5262 - DPBO - DPBO:1000183 - biological replicate group + + + An unique identifier for grouping biological replicates - replicates made from different individual biosamples to assess biological variation in an experiment. In contrast to other ways of annotating replicates in experimental design, biological replicate groups must be the same for each replicate in the group (e.g. 'b_1' for each biological replicate in the group). This adds the possibility to aggregate the biological replicates without additional annotations. + Kevin Schneider | ORCID: 0000-0002-2198-5262 + DPBO + DPBO:1000183 + biological replicate group - + - - - An unique identifier for grouping technical replicates - replicates made from different individual biosamples to assess technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, technical replicate groups must be the same for each replicate in the group (e.g. 't_1' for each technical replicate in the group). This adds the possibility to aggregate the technical replicates without additional annotations. - Kevin Schneider | ORCID: 0000-0002-2198-526 - DPBO - DPBO:1000184 - technical replicate group + + + An unique identifier for grouping technical replicates - replicates made from different individual biosamples to assess technical variation in an experiment. In contrast to other ways of annotating replicates in experimental design, technical replicate groups must be the same for each replicate in the group (e.g. 't_1' for each technical replicate in the group). This adds the possibility to aggregate the technical replicates without additional annotations. + Kevin Schneider | ORCID: 0000-0002-2198-526 + DPBO + DPBO:1000184 + technical replicate group - + - - The time that a sample should incubate (keep at a suitable temperature) during a experimental protocol to allow for a reaction or proces to occur. - Kathryn Dumschott | ORCID: 0000-0002-9905-401 - BAO:0002833 - DPBO - DPBO:1000185 - incubation time + + The time that a sample should incubate (keep at a suitable temperature) during a experimental protocol to allow for a reaction or proces to occur. + Kathryn Dumschott | ORCID: 0000-0002-9905-401 + BAO:0002833 + DPBO + DPBO:1000185 + incubation time - + - + - Axiovert series, inverse microscope - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000186 - Zeiss Axiovert + Axiovert series, inverse microscope + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000186 + Zeiss Axiovert - + - + - binocular, stereo microscope - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000187 - Olympus SZX7 (Bino) + binocular, stereo microscope + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000187 + Olympus SZX7 (Bino) - + - + - camera - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000188 - Zeiss AxioCam MRc5 + camera + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000188 + Zeiss AxioCam MRc5 - + - - - white - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000189 - 01 + + + white + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000189 + 01 - + - - - white - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000190 - 01 + + + white + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000190 + 01 - + - - - differential interference contrast - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000191 - DIC + + + differential interference contrast + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000191 + DIC - + - - - yellow - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000192 - 09 + + + yellow + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000192 + 09 - + - - - green - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000193 - 10 + + + green + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000193 + 10 - + - - - red - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000194 - 15 + + + red + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000194 + 15 - + - + - software controlling imaging systems from ZEISS. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000195 - Zeiss ZEN 3.5 (blue edition) + software controlling imaging systems from ZEISS. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000195 + Zeiss ZEN 3.5 (blue edition) - + - + - microscope slide - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000196 - Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm + microscope slide + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000196 + Thermo Scientific Menzel slides, 76 x 26 mm, 1,0 mm - + - + - microscope slide - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000197 - VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm + microscope slide + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000197 + VWR frosted edges, ground edges 90°, 76 x 26 mm, 0,8 - 1,0 mm - + - + - microscope slide - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000198 - Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm + microscope slide + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000198 + Roth SuperFrost® white, cut edges, 76 x 26 mm, 1,0 mm - + - + - cover slip - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000199 - Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5 + cover slip + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000199 + Menzel, 24 x 50 mm, selected 0,17 +/- 0,01, strength 1,5 - + - + - cover slip - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000200 - Roth, 24 x 50 mm, strength 1 + cover slip + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000200 + Roth, 24 x 50 mm, strength 1 - + - + - cover slip - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000201 - VWR, 18 x 18 mm, 0,13 - 0,16 mm, strength 1,5 + cover slip + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000201 + VWR, 18 x 18 mm, 0,13 - 0,16 mm, strength 1,5 - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000202 - 0.8x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000202 + 0.8x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000203 - 1x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000203 + 1x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000204 - 1.25x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000204 + 1.25x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000205 - 1.6x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000205 + 1.6x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000206 - 2x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000206 + 2x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000207 - 2.5x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000207 + 2.5x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000208 - 3.2x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000208 + 3.2x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000209 - 4x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000209 + 4x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000210 - 5x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000210 + 5x - + - - - magnification of Olympus SZX7 (Bino) - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000211 - 5.6x + + + magnification of Olympus SZX7 (Bino) + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000211 + 5.6x - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000212 - Plan-Neofluar 5x/0.15 + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000212 + Plan-Neofluar 5x/0.15 - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000213 - Plan-Neofluar 10x/0.3 + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000213 + Plan-Neofluar 10x/0.3 - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000214 - Plan-Neofluar 20x/0.50 Ph2 + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000214 + Plan-Neofluar 20x/0.50 Ph2 - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000215 - Plan-Neofluar 40x/0.75 + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000215 + Plan-Neofluar 40x/0.75 - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000216 - Plan-Neofluar 63x/1.25 Oil + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000216 + Plan-Neofluar 63x/1.25 Oil - + - + - objective lens of Zeiss Axioplan 2 - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000217 - Plan-Neofluar 100x/1.30 Oil + objective lens of Zeiss Axioplan 2 + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000217 + Plan-Neofluar 100x/1.30 Oil - + - + - objective lens of Zeiss Axiovert - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000218 - Achroplan 5x/012 + objective lens of Zeiss Axiovert + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000218 + Achroplan 5x/012 - + - + - objective lens of Zeiss Axiovert - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000219 - Achroplan 10x/0.25 Ph1 + objective lens of Zeiss Axiovert + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000219 + Achroplan 10x/0.25 Ph1 - + - + - objective lens of Zeiss Axiovert - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000220 - Achroplan 20x/0.40 + objective lens of Zeiss Axiovert + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000220 + Achroplan 20x/0.40 - + - + - objective lens of Zeiss Axiovert - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000221 - Achroplan 40x/0.60 korr Ph2 + objective lens of Zeiss Axiovert + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000221 + Achroplan 40x/0.60 korr Ph2 - + - + - objective lens of Zeiss Axiovert - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000222 - Achroplan 63x/0.75 korr Ph2 + objective lens of Zeiss Axiovert + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000222 + Achroplan 63x/0.75 korr Ph2 - + - + - A solution designed for the growth of plant cell, tissue and organ culture. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - Knop ME - Knop solution - DPBO:1000223 - Knop medium + A solution designed for the growth of plant cell, tissue and organ culture. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + Knop ME + Knop solution + DPBO:1000223 + Knop medium - + - - The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype. - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000224 - Definition from https://www.merriam-webster.com/dictionary/phenotyping - phenotyping + + The activity or process of determining, analyzing, or predicting all or part of an organism's phenotype. + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000224 + Definition from https://www.merriam-webster.com/dictionary/phenotyping + phenotyping - + - + - Axioplan series, imaging fluorescence microscope - Kathryn Dumschott | ORCID: 0000-0002-9905-4011 - DPBO - DPBO:1000225 - NOTE: This term's ID has been changed from DPBO:1000185 to DPBO:1000225 due to a discrepancy with the term ID: the ID DPBO:1000185 was already being used for another term within the ontology (incubation time) - Zeiss Axioplan 2 + Axioplan series, imaging fluorescence microscope + Kathryn Dumschott | ORCID: 0000-0002-9905-4011 + DPBO + DPBO:1000225 + NOTE: This term's ID has been changed from DPBO:1000185 to DPBO:1000225 due to a discrepancy with the term ID: the ID DPBO:1000185 was already being used for another term within the ontology (incubation time) + Zeiss Axioplan 2 - + - - A role of a student in a research project which is acknowledged in papers. - Andrea Schrader | 0000-0002-3879-7057 - DPBO - DPBO:1000226 - student helper + + A role of a student in a research project which is acknowledged in papers. + Andrea Schrader | 0000-0002-3879-7057 + DPBO + DPBO:1000226 + student helper - + - - A person that helps at various steps of the plant growth cycle e.g. sowing seeds, separating plants at the correct age or collecting seeds. - DPBO - DPBO:1000227 - Suggested by Andrea Schrader | 0000-0002-3879-7057 - plant work helper + + A person that helps at various steps of the plant growth cycle e.g. sowing seeds, separating plants at the correct age or collecting seeds. + DPBO + DPBO:1000227 + Suggested by Andrea Schrader | 0000-0002-3879-7057 + plant work helper - + - - A method for physical delivery of DNA (likely also RNA) into cells. Gold or tungsten particles are coated with DNA and shot with a gene gun / particle gun on tissue like leaves, seedlings, callus or other types of tissue and cells. Often, in plant sciences, this method is used as a transient transformation method in protein or protein-protein interaction localization studies using binary vectors. Co-transformation of multiple vectors is possible. - particle bombardment - DPBO - DPBO:1000228 - Suggested by Andrea Schrader | 0000-0002-3879-7057 - biolistic transformation + + A method for physical delivery of DNA (likely also RNA) into cells. Gold or tungsten particles are coated with DNA and shot with a gene gun / particle gun on tissue like leaves, seedlings, callus or other types of tissue and cells. Often, in plant sciences, this method is used as a transient transformation method in protein or protein-protein interaction localization studies using binary vectors. Co-transformation of multiple vectors is possible. + particle bombardment + DPBO + DPBO:1000228 + Suggested by Andrea Schrader | 0000-0002-3879-7057 + biolistic transformation - + - - A protocol describing the method of a bioimaging technique. Bioimaging is a biological imaging method causing as minimal interference to living processes as possible or getting a 3-D structure from the outside without physical interference e.g. of cells, tissues or other living matter. Usually, the method is non-invasive but also fixed biological material is covered by a wider definition. (adapted from https://cab.ku.dk/what_is_bioimaging/) - DPBO - DPBO:1000229 - Suggested by Andrea Schrader | 0000-0002-3879-7057 - bioimaging protocol + + A protocol describing the method of a bioimaging technique. Bioimaging is a biological imaging method causing as minimal interference to living processes as possible or getting a 3-D structure from the outside without physical interference e.g. of cells, tissues or other living matter. Usually, the method is non-invasive but also fixed biological material is covered by a wider definition. (adapted from https://cab.ku.dk/what_is_bioimaging/) + DPBO + DPBO:1000229 + Suggested by Andrea Schrader | 0000-0002-3879-7057 + bioimaging protocol - + - - A protocol describing a transformation method of cell, tissues or organisms. - DPBO - DPBO:1000230 - Suggested by Andrea Schrader | 0000-0002-3879-7057 - transformation protocol + + A protocol describing a transformation method of cell, tissues or organisms. + DPBO + DPBO:1000230 + Suggested by Andrea Schrader | 0000-0002-3879-7057 + transformation protocol - + - + - Inverted fluorescence microscope - suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 - DPBO - DPBO:1000231 - https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html - Zeiss Axio Observer Z1 + Inverted fluorescence microscope + suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 + DPBO + DPBO:1000231 + https://www.zeiss.com/microscopy/en/products/light-microscopes/widefield-microscopes/axio-observer-for-life-science-research.html + Zeiss Axio Observer Z1 - + - + - Upright fluorescence microscope - suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 - DPBO - DPBO:1000232 - https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop - Zeiss Imager M1 + Upright fluorescence microscope + suggested by Ursula Eberhardt | ORCID: 0000-0003-1221-7074 + DPBO + DPBO:1000232 + https://microscopy.ucsf.edu/instruments/zeiss-axioimager-m1, https://profcontrol.de/Zeiss-Axio-Imager-M1m-Fluorescence-DIC-Microscope-Fluoreszenz-Mikroskop + Zeiss Imager M1 - + - - A data field which describes the MG-RAST identifier linking raw read data, methodological metadata and quality control metrics submitted to the MG-RAST metagenomics analysis server. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000233 - https://www.mg-rast.org/mgmain.html?mgpage=analysis - MG-RAST accession number field + + A data field which describes the MG-RAST identifier linking raw read data, methodological metadata and quality control metrics submitted to the MG-RAST metagenomics analysis server. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000233 + https://www.mg-rast.org/mgmain.html?mgpage=analysis + MG-RAST accession number field - + - - Tool/Software used for assembly. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000234 - https://genomicsstandardsconsortium.github.io/mixs/0000058/ - assembly software + + Tool/Software used for assembly. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000234 + https://genomicsstandardsconsortium.github.io/mixs/0000058/ + assembly software - + - - Parameters used for assembly. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000235 - https://genomicsstandardsconsortium.github.io/mixs/0000058/ - assembly parameters + + Parameters used for assembly. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000235 + https://genomicsstandardsconsortium.github.io/mixs/0000058/ + assembly parameters - + - - The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000236 - https://genomicsstandardsconsortium.github.io/mixs/0000056/ - MISAG/MIMAG assembly quality + + The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000236 + https://genomicsstandardsconsortium.github.io/mixs/0000056/ + MISAG/MIMAG assembly quality - + - - Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000237 - https://genomicsstandardsconsortium.github.io/mixs/0000078/ - binning software + + Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000237 + https://genomicsstandardsconsortium.github.io/mixs/0000078/ + binning software - + - - The parameters that have been applied during the extraction of genomes from metagenomic datasets. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000238 - https://genomicsstandardsconsortium.github.io/mixs/0000077/ - binning parameters + + The parameters that have been applied during the extraction of genomes from metagenomic datasets. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000238 + https://genomicsstandardsconsortium.github.io/mixs/0000077/ + binning parameters - + - - The phylogenetic marker(s) used to assign an organism name to the SAG or MAG. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000239 - https://genomicsstandardsconsortium.github.io/mixs/0000053/ - taxonomic identity marker + + The phylogenetic marker(s) used to assign an organism name to the SAG or MAG. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000239 + https://genomicsstandardsconsortium.github.io/mixs/0000053/ + taxonomic identity marker - + - - Tools used for completion estimate, i.e. checkm, anvi'o, busco. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000240 - https://genomicsstandardsconsortium.github.io/mixs/0000070/ - completeness software + + Tools used for completion estimate, i.e. checkm, anvi'o, busco. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000240 + https://genomicsstandardsconsortium.github.io/mixs/0000070/ + completeness software - + - - Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores. - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000241 - https://genomicsstandardsconsortium.github.io/mixs/0000069/ - completeness score + + Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores. + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000241 + https://genomicsstandardsconsortium.github.io/mixs/0000069/ + completeness score - + - - The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases - Angela Kranz | ORCID: 0000-0002-8000-0400 - DPBO - DPBO:1000242 - https://genomicsstandardsconsortium.github.io/mixs/0000072/ - contamination score + + The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases + Angela Kranz | ORCID: 0000-0002-8000-0400 + DPBO + DPBO:1000242 + https://genomicsstandardsconsortium.github.io/mixs/0000072/ + contamination score @@ -6350,19 +6344,19 @@ - An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. - Spectroscopy - NMR spectroscopy - Nuclear magnetic resonance spectroscopy - HOESY - Heteronuclear Overhauser Effect Spectroscopy - NOESY - Nuclear Overhauser Effect Spectroscopy - ROESY - Rotational Frame Nuclear Overhauser Effect Spectroscopy - DPBO - EDAM:0593 - NMR + An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. + Spectroscopy + NMR spectroscopy + Nuclear magnetic resonance spectroscopy + HOESY + Heteronuclear Overhauser Effect Spectroscopy + NOESY + Nuclear Overhauser Effect Spectroscopy + ROESY + Rotational Frame Nuclear Overhauser Effect Spectroscopy + DPBO + EDAM:0593 + NMR @@ -6370,11 +6364,11 @@ - - FASTQ short read format ignoring quality scores. - DPBO - EDAM:1930 - FASTQ + + FASTQ short read format ignoring quality scores. + DPBO + EDAM:1930 + FASTQ @@ -6382,10 +6376,10 @@ - - DPBO - EFO:0000490 - extraction protocol + + DPBO + EFO:0000490 + extraction protocol @@ -6393,9 +6387,9 @@ - DPBO - EFO:0000568 - light + DPBO + EFO:0000568 + light @@ -6404,11 +6398,11 @@ - ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins. - NCIt:C106049 - DPBO - EFO:0002692 - ChIP-seq + ChIP-seq is an assay in which chromatin immunoprecipitation with high throughput sequencing is used to identify the cistrome of DNA-associated proteins. + NCIt:C106049 + DPBO + EFO:0002692 + ChIP-seq @@ -6416,10 +6410,10 @@ - A process performed as part of an experiment or wider study, i.e. intentionally designed. - DPBO - EFO:0002694 - experimental process + A process performed as part of an experiment or wider study, i.e. intentionally designed. + DPBO + EFO:0002694 + experimental process @@ -6428,11 +6422,11 @@ - An assay in which DNA us the input molecule derived from cleavage of DNA by use of methylation sensitive restriction enzymes to fragment DNA at methylation sites before sequencing - Methylation-Sensitive Restriction Enzyme sequencing - DPBO - EFO:0003748 - MRE-seq + An assay in which DNA us the input molecule derived from cleavage of DNA by use of methylation sensitive restriction enzymes to fragment DNA at methylation sites before sequencing + Methylation-Sensitive Restriction Enzyme sequencing + DPBO + EFO:0003748 + MRE-seq @@ -6441,11 +6435,11 @@ - An assay in which DNA is the input molecule derived from an antibody based selection process using antibodies targeting methylated DNA, which is then sequenced using high throughput sequencing technology. - Methylated DNA Immunoprecipitation sequencing - DPBO - EFO:0003749 - MeDIP-seq + An assay in which DNA is the input molecule derived from an antibody based selection process using antibodies targeting methylated DNA, which is then sequenced using high throughput sequencing technology. + Methylated DNA Immunoprecipitation sequencing + DPBO + EFO:0003749 + MeDIP-seq @@ -6454,11 +6448,11 @@ - An assay in which DNA is the input molecule derived from a selection process using methyl binding domain protein to enrich for methylated fractions of DNA, then sequenced using high throughput sequencing. - methyl binding domain sequencing - DPBO - EFO:0003750 - MBD-seq + An assay in which DNA is the input molecule derived from a selection process using methyl binding domain protein to enrich for methylated fractions of DNA, then sequenced using high throughput sequencing. + methyl binding domain sequencing + DPBO + EFO:0003750 + MBD-seq @@ -6467,10 +6461,10 @@ - An assay in which DNA is the input molecule derived from a micrococcal nuclease digestion followed by high throughput sequencing, A method that distinguishes nucleosome positioning based on the ability of nucleosomes to protect associated DNA from digestion by micrococcal nuclease. Sequenced fragments reveal nucleosome location information about the input DNA. - DPBO - EFO:0003751 - MNase-seq + An assay in which DNA is the input molecule derived from a micrococcal nuclease digestion followed by high throughput sequencing, A method that distinguishes nucleosome positioning based on the ability of nucleosomes to protect associated DNA from digestion by micrococcal nuclease. Sequenced fragments reveal nucleosome location information about the input DNA. + DPBO + EFO:0003751 + MNase-seq @@ -6479,10 +6473,10 @@ - An assay in which DNA is the input molecule derived from a bisulphite treatment of DNA to convert cytosine residues to uracil to determine methylation status. - DPBO - EFO:0003753 - Bisulfite-seq + An assay in which DNA is the input molecule derived from a bisulphite treatment of DNA to convert cytosine residues to uracil to determine methylation status. + DPBO + EFO:0003753 + Bisulfite-seq @@ -6490,10 +6484,10 @@ - - DPBO - EFO:0003789 - growth protocol + + DPBO + EFO:0003789 + growth protocol @@ -6501,10 +6495,10 @@ - - DPBO - EFO:0003969 - treatment protocol + + DPBO + EFO:0003969 + treatment protocol @@ -6512,11 +6506,11 @@ - - A DNA sequencer developed by Illumina. - DPBO - EFO:0004202 - Illumina Genome Analyzer IIx + + A DNA sequencer developed by Illumina. + DPBO + EFO:0004202 + Illumina Genome Analyzer IIx @@ -6524,11 +6518,11 @@ - - The Illumina HiSeq 2000 is a sequencing machine developed by Illumina. - DPBO - EFO:0004203 - Illumina HiSeq 2000 + + The Illumina HiSeq 2000 is a sequencing machine developed by Illumina. + DPBO + EFO:0004203 + Illumina HiSeq 2000 @@ -6536,11 +6530,11 @@ - - The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions and 16S metagenomic sequencing. - DPBO - EFO:0004205 - Illumina MiSeq + + The Illumina MiSeq is a high-throughput sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions and 16S metagenomic sequencing. + DPBO + EFO:0004205 + Illumina MiSeq @@ -6548,11 +6542,11 @@ - - The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences. - DPBO - EFO:0004206 - 454 GS 20 sequencer + + The 454 GS 20 is a GS20 high-throughput sequencing machine developed by 454 Life Sciences. + DPBO + EFO:0004206 + 454 GS 20 sequencer @@ -6561,11 +6555,11 @@ - FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is an assay used for determining the sequences of DNA regions associated with regulatory activity. This is enabled by the isolation of nucleosome-depleted DNA from total genomic dna to access actively transcribed dna. - NCIt:C106051 - DPBO - EFO:0004428 - FAIRE-seq + FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements) is an assay used for determining the sequences of DNA regions associated with regulatory activity. This is enabled by the isolation of nucleosome-depleted DNA from total genomic dna to access actively transcribed dna. + NCIt:C106051 + DPBO + EFO:0004428 + FAIRE-seq @@ -6573,11 +6567,11 @@ - - The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences. - DPBO - EFO:0004431 - 454 GS sequencer + + The 454 GS is a GS high-throughput sequencing machine developed by 454 Life Sciences. + DPBO + EFO:0004431 + 454 GS sequencer @@ -6585,10 +6579,10 @@ - - DPBO - EFO:0004432 - 454 GS FLX sequencer + + DPBO + EFO:0004432 + 454 GS FLX sequencer @@ -6596,11 +6590,11 @@ - - The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences. - DPBO - EFO:0004433 - 454 GS FLX Titanium sequencer + + The 454 GS FLX Titanium sequencer is a GS high-throughput sequencing machine developed by 454 Life Sciences. + DPBO + EFO:0004433 + 454 GS FLX Titanium sequencer @@ -6608,11 +6602,11 @@ - - The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences. - DPBO - EFO:0004434 - 454 GS Junior sequencer + + The 454 GS Junior is a GS high-throughput sequencing machine developed by 454 Life Sciences. + DPBO + EFO:0004434 + 454 GS Junior sequencer @@ -6620,10 +6614,10 @@ - - DPBO - EFO:0004437 - AB SOLiD PI System + + DPBO + EFO:0004437 + AB SOLiD PI System @@ -6631,10 +6625,10 @@ - - DPBO - EFO:0004438 - AB SOLiD 4 System + + DPBO + EFO:0004438 + AB SOLiD 4 System @@ -6642,10 +6636,10 @@ - - DPBO - EFO:0004439 - AB SOLiD System 3.0 + + DPBO + EFO:0004439 + AB SOLiD System 3.0 @@ -6653,10 +6647,10 @@ - - DPBO - EFO:0004441 - AB SOLiD 4hq System + + DPBO + EFO:0004441 + AB SOLiD 4hq System @@ -6664,10 +6658,10 @@ - - DPBO - EFO:0004442 - AB SOLiD System 2.0 + + DPBO + EFO:0004442 + AB SOLiD System 2.0 @@ -6675,11 +6669,11 @@ - - An RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimen. - DPBO - EFO:0004964 - total RNA + + An RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimen. + DPBO + EFO:0004964 + total RNA @@ -6687,10 +6681,10 @@ - A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. - DPBO - EFO:0005135 - strain + A population of organisms that is geneticaly different from others of the same species and possessing a set of defined characteristics. + DPBO + EFO:0005135 + strain @@ -6699,10 +6693,10 @@ - A method used for finding which RNA species interact with a particular RNA-binding protein. It involves immunoprecipitation with antibodies for the protein and then isolation of the RNAs associated with the protein. Unlike CLIP-seq, no cross-linking of RNAs and proteins is carried out prior to immunoprecipitation. - DPBO - EFO:0005310 - RIP-seq + A method used for finding which RNA species interact with a particular RNA-binding protein. It involves immunoprecipitation with antibodies for the protein and then isolation of the RNAs associated with the protein. Unlike CLIP-seq, no cross-linking of RNAs and proteins is carried out prior to immunoprecipitation. + DPBO + EFO:0005310 + RIP-seq @@ -6710,10 +6704,10 @@ - - DPBO - EFO:0005518 - sample collection protocol + + DPBO + EFO:0005518 + sample collection protocol @@ -6722,11 +6716,11 @@ - Assay for transposase-accessible chromatin using sequencing (ATAC-seq), is a method based on direct in vitro transposition of sequencing adaptors into native chromatin, and is a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol. - http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html - DPBO - EFO:0007045 - ATAC-seq + Assay for transposase-accessible chromatin using sequencing (ATAC-seq), is a method based on direct in vitro transposition of sequencing adaptors into native chromatin, and is a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol. + http://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html + DPBO + EFO:0007045 + ATAC-seq @@ -6735,10 +6729,10 @@ - Hi-C is a method for analysing 3-dimensional organisation and interaction of chromatin, belonging to the class of techniques collectively called "Chromosome Conformation Capture", in which chromatin is crosslinked, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. Together with 5C, Hi-C does not limit to the study to a specific locus in the genome, and can be used to study chromatin interaction across the genome. To achieve high-throughput, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. Mapping the sequenced reads back to genome will reveal the origin of the fragments involved in the ligation events. - DPBO - EFO:0007693 - Hi-C + Hi-C is a method for analysing 3-dimensional organisation and interaction of chromatin, belonging to the class of techniques collectively called "Chromosome Conformation Capture", in which chromatin is crosslinked, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. Together with 5C, Hi-C does not limit to the study to a specific locus in the genome, and can be used to study chromatin interaction across the genome. To achieve high-throughput, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. Mapping the sequenced reads back to genome will reveal the origin of the fragments involved in the ligation events. + DPBO + EFO:0007693 + Hi-C @@ -6746,11 +6740,11 @@ - - The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina. - DPBO - EFO:0008563 - Illumina HiSeq 4000 + + The Illumina HiSeq 4000 is a high-throughput sequencing machine developed by Illumina. + DPBO + EFO:0008563 + Illumina HiSeq 4000 @@ -6758,11 +6752,11 @@ - - The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina. - DPBO - EFO:0008564 - Illumina HiSeq 3000 + + The Illumina HiSeq 3000 is a high-throughput sequencing machine developed by Illumina. + DPBO + EFO:0008564 + Illumina HiSeq 3000 @@ -6770,11 +6764,11 @@ - - The Illumina HiSeq 2500 is a sequencing machine developed by Illumina. - DPBO - EFO:0008565 - Illumina HiSeq 2500 + + The Illumina HiSeq 2500 is a sequencing machine developed by Illumina. + DPBO + EFO:0008565 + Illumina HiSeq 2500 @@ -6782,11 +6776,11 @@ - - The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina. Its primary applications include exome sequencing, targeted gene sequencing (amplicon, gene panel), whole-transcriptome sequencing and cytogenomic arrays. - DPBO - EFO:0008566 - Illumina NextSeq 550 + + The Illumina NextSeq 550 is a benchtop high-throughput sequencing machine developed by Illumina. Its primary applications include exome sequencing, targeted gene sequencing (amplicon, gene panel), whole-transcriptome sequencing and cytogenomic arrays. + DPBO + EFO:0008566 + Illumina NextSeq 550 @@ -6794,11 +6788,11 @@ - - The PacBio RS II is a high-throughput sequencing machine developed by PacBio. Its primary applications are whole genome sequencing of smaller organisms and targeted sequencing of DNA and RNA. - DPBO - EFO:0008631 - PacBio RS II + + The PacBio RS II is a high-throughput sequencing machine developed by PacBio. Its primary applications are whole genome sequencing of smaller organisms and targeted sequencing of DNA and RNA. + DPBO + EFO:0008631 + PacBio RS II @@ -6806,11 +6800,11 @@ - - The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies. - DPBO - EFO:0008632 - ONT MinION + + The ONT MinION is a pocket-sized sequencing machine developed by Oxford Nanopore Technologies. + DPBO + EFO:0008632 + ONT MinION @@ -6818,11 +6812,11 @@ - - The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. - DPBO - EFO:0008635 - Illumina iSeq 100 + + The Illumina iSeq 100 is a benchtop sequencing machine developed by Illumina. Its primary applications include small whole-genome sequencing, targeted sequencing of a set of genes or gene regions, gene expression analysis and 16S metagenomic sequencing. + DPBO + EFO:0008635 + Illumina iSeq 100 @@ -6830,11 +6824,11 @@ - - The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina. - DPBO - EFO:0008636 - Illumina MiniSeq + + The Illumina MiniSeq is a benchtop sequencing machine developed by Illumina. + DPBO + EFO:0008636 + Illumina MiniSeq @@ -6842,11 +6836,11 @@ - - The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina. - DPBO - EFO:0008637 - Illumina NovaSeq 6000 + + The Illumina NovaSeq 6000 is a high-throughput sequencing machine developed by Illumina. + DPBO + EFO:0008637 + Illumina NovaSeq 6000 @@ -6855,12 +6849,12 @@ - ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) is a type of chromosome conformation capture assay that uses chromatin immunoprecipitation to enrich for protein-specific chromatin complexes after digestion, followed by nuclear proximity ligation and high-throughput paired-end-tag sequencing. - PMID:20181287 - chromatin interaction analysis by paired-end tag sequencing - DPBO - EFO:0008684 - Chia-PET + ChIA-PET (chromatin interaction analysis by paired-end tag sequencing) is a type of chromosome conformation capture assay that uses chromatin immunoprecipitation to enrich for protein-specific chromatin complexes after digestion, followed by nuclear proximity ligation and high-throughput paired-end-tag sequencing. + PMID:20181287 + chromatin interaction analysis by paired-end tag sequencing + DPBO + EFO:0008684 + Chia-PET @@ -6869,12 +6863,12 @@ - RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing. - Dani Welter - PMID:18516045 - DPBO - EFO:0008896 - RNA-Seq + RNA-seq is a method that involves purifying RNA and making cDNA, followed by high-throughput sequencing. + Dani Welter + PMID:18516045 + DPBO + EFO:0008896 + RNA-Seq @@ -6883,12 +6877,12 @@ - Strand-specific RNA-seq (ssRNA-seq) - Dani Welter - PMID:19609351 - DPBO - EFO:0008950 - ssRNA-seq + Strand-specific RNA-seq (ssRNA-seq) + Dani Welter + PMID:19609351 + DPBO + EFO:0008950 + ssRNA-seq @@ -6897,12 +6891,12 @@ - Transposon sequencing (TN-Seq) - Dani Welter - PMID:23712350 - DPBO - EFO:0008973 - TN-Seq + Transposon sequencing (TN-Seq) + Dani Welter + PMID:23712350 + DPBO + EFO:0008973 + TN-Seq @@ -6910,11 +6904,11 @@ - - The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina. - DPBO - EFO:0009173 - Illumina NextSeq 500 + + The Illumina NextSeq 500 is a benchtop high-throughput sequencing machine developed by Illumina. + DPBO + EFO:0009173 + Illumina NextSeq 500 @@ -6923,9 +6917,9 @@ - DPBO - EFO:0010959 - RNA extraction protocol + DPBO + EFO:0010959 + RNA extraction protocol @@ -6933,11 +6927,11 @@ - - The Illumina HiSeq 1500 is a sequencing machine developed by Illumina. - DPBO - EFO:0011027 - Illumina HiSeq 1500 + + The Illumina HiSeq 1500 is a sequencing machine developed by Illumina. + DPBO + EFO:0011027 + Illumina HiSeq 1500 @@ -6946,9 +6940,9 @@ - DPBO - EFO:0022383 - protein extraction protocol + DPBO + EFO:0022383 + protein extraction protocol @@ -6957,9 +6951,9 @@ - DPBO - EFO:0022384 - DNA extraction protocol + DPBO + EFO:0022384 + DNA extraction protocol @@ -6967,10 +6961,10 @@ - - DPBO - EFO:0030052 - nuclear RNA + + DPBO + EFO:0030052 + nuclear RNA @@ -6978,11 +6972,11 @@ - - A hot spring that erupts periodically, ejecting a column of hot water and steam into the air. - DPBO - ENVO:00000050 - geyser + + A hot spring that erupts periodically, ejecting a column of hot water and steam into the air. + DPBO + ENVO:00000050 + geyser @@ -6990,11 +6984,11 @@ - - A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor. - DPBO - ENVO:01000263 - cold seep + + A cold seep is a seep in which methane and other hydrocarbon-rich fluids rise to the sea floor. + DPBO + ENVO:01000263 + cold seep @@ -7002,11 +6996,11 @@ - - This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified. - DPBO - ENVO:01000403 - tropical mangrove + + This class corresponds to the 'Tropical Mixed needleleaf / broadleaf forest' category of the updated Global Forest Map classification (GFM 2000). To reconstruct the original class, an aggregate class with this and the 'tropical mixed needleleaf forest' class can be made. The relationship between this 'forest' class and the mangrove swamp must be clarified. + DPBO + ENVO:01000403 + tropical mangrove @@ -7014,10 +7008,10 @@ - Any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or a set of characteristics or parameters related to the image. - DPBO - ERO:0001788 - image processing technique + Any form of signal processing for which the input is an image, such as a photograph or video frame; the output of image processing may be either an image or a set of characteristics or parameters related to the image. + DPBO + ERO:0001788 + image processing technique @@ -7025,10 +7019,10 @@ - Anatomical or other piece(s) or substance derived from one or more plants. - DPBO - FOODON:00004331 - plant material + Anatomical or other piece(s) or substance derived from one or more plants. + DPBO + FOODON:00004331 + plant material @@ -7036,10 +7030,10 @@ - Numbers of base pairs per read - DPBO - GENEPIO:0000076 - read length + Numbers of base pairs per read + DPBO + GENEPIO:0000076 + read length @@ -7047,10 +7041,10 @@ - Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters. - DPBO - GENEPIO:0000083 - adapter sequence + Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters. + DPBO + GENEPIO:0000083 + adapter sequence @@ -7058,10 +7052,10 @@ - Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. - DPBO - GENEPIO:0000085 - library preparation kit + Packaged kits (containing adapters, indexes, enzymes, buffers etc), tailored for specific sequencing workflows, which allow the simplified preparation of sequencing-ready libraries for small genomes, amplicons, and plasmids. + DPBO + GENEPIO:0000085 + library preparation kit @@ -7069,10 +7063,10 @@ - The version identifier of a packaged kit tailored for specific sequencing workflows. - DPBO - GENEPIO:0000149 - library preparation kit version + The version identifier of a packaged kit tailored for specific sequencing workflows. + DPBO + GENEPIO:0000149 + library preparation kit version @@ -7080,22 +7074,22 @@ - SRR11177792 + SRR11177792 - A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC). - SRA accession - SRA_accession - https://orcid.org/0000-0002-1107-9135 - https://orcid.org/0000-0002-8844-9165 - https://orcid.org/0000-0002-9578-0788 + A data field which describes the Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the International Nucleotide Sequence Database Collaboration (INSDC). + SRA accession + SRA_accession + https://orcid.org/0000-0002-1107-9135 + https://orcid.org/0000-0002-8844-9165 + https://orcid.org/0000-0002-9578-0788 2021-04-24T00:42:14Z - SRA accession slot - Sequence Read Archive accession field - Sequence Read Archive accession slot - DPBO - GENEPIO:0001142 - DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. - SRA accession field + SRA accession slot + Sequence Read Archive accession field + Sequence Read Archive accession slot + DPBO + GENEPIO:0001142 + DDBJ = DNA DataBank of Japan Example Guidance: Store the accession assigned to the submitted .run.. NCBI-SRA accessions start with SRR, EBI-ENA runs start with ERR and DRA accessions start with DRR. + SRA accession field @@ -7103,11 +7097,11 @@ - The name of the agency that collected the original sample. - NCIT:C45262 - DPBO - GENEPIO:0001153 - sample collected by + The name of the agency that collected the original sample. + NCIT:C45262 + DPBO + GENEPIO:0001153 + sample collected by @@ -7115,11 +7109,11 @@ - The date on which the sample was collected - NCIT:C81286 - DPBO - GENEPIO:0001174 - sample collection date + The date on which the sample was collected + NCIT:C81286 + DPBO + GENEPIO:0001174 + sample collection date @@ -7127,9 +7121,9 @@ - DPBO - GENEPIO:0001681 - laboratory sequencing datum + DPBO + GENEPIO:0001681 + laboratory sequencing datum @@ -7137,11 +7131,11 @@ - - Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: 'Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).' - DPBO - GENEPIO:0001924 - Complete Genomics platform + + Damion Dooley's note: This platform is in-house and not a product per se. Complete Genomics states: 'Complete Genomics’ sequencing platform employs high-density DNA nanoarrays that are populated with DNA nanoballs (DNBs™). Base identification is performed using an unchained ligation-based read technology known as combinatorial probe-anchor ligation (cPAL™). The sequencing instrumentation is custom-developed to support this process. Details are described in our Science publication (Drmanac et al., 2010).' + DPBO + GENEPIO:0001924 + Complete Genomics platform @@ -7149,10 +7143,10 @@ - - DPBO - GENEPIO:0001928 - SOLiD 4hq System + + DPBO + GENEPIO:0001928 + SOLiD 4hq System @@ -7160,10 +7154,10 @@ - - DPBO - GENEPIO:0001931 - SOLiD PI System + + DPBO + GENEPIO:0001931 + SOLiD PI System @@ -7171,10 +7165,10 @@ - - DPBO - GENEPIO:0001932 - SOLiD System 2.0 + + DPBO + GENEPIO:0001932 + SOLiD System 2.0 @@ -7182,10 +7176,10 @@ - - DPBO - GENEPIO:0001933 - SOLiD System 3.0 + + DPBO + GENEPIO:0001933 + SOLiD System 3.0 @@ -7193,10 +7187,10 @@ - - DPBO - GENEPIO:0001936 - 454 Genome Sequencer FLX Titanium + + DPBO + GENEPIO:0001936 + 454 Genome Sequencer FLX Titanium @@ -7204,10 +7198,10 @@ - - DPBO - GENEPIO:0001938 - 454 Genome Sequencer Junior + + DPBO + GENEPIO:0001938 + 454 Genome Sequencer Junior @@ -7216,13 +7210,325 @@ - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - Whether any method was used to select for or against, enrich, or screen the material being sequenced. - Damion Dooley - NCBI SRA: LIBRARY_SELECTION - DPBO - GENEPIO:0001940 - library selection + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + Whether any method was used to select for or against, enrich, or screen the material being sequenced. + Damion Dooley + NCBI SRA: LIBRARY_SELECTION + DPBO + GENEPIO:0001940 + library selection + + + + + + + + + Selection of methylated DNA fragments using an antibody raised against 5-methylcytosine or 5-methylcytidine (m5C). + NCBI SRA: 5-methylcytidine antibody + DPBO + GENEPIO:0001941 + 5-methylcytidine antibody method + + + + + + + + + Cap-analysis gene expression. + NCBI SRA: CAGE + DPBO + GENEPIO:0001942 + CAGE method + + + + + + + + + Cot-filtered highly repetitive genomic DNA + NCBI SRA: CF-H + DPBO + GENEPIO:0001943 + CF-H method + + + + + + + + + Cot-filtered moderately repetitive genomic DNA + NCBI SRA: CF-M + DPBO + GENEPIO:0001944 + CF-M method + + + + + + + + + Cot-filtered single/low-copy genomic DNA + NCBI SRA: CF-S + DPBO + GENEPIO:0001945 + CF-S method + + + + + + + + + Cot-filtered theoretical single-copy genomic DNA + NCBI SRA: CF-T + DPBO + GENEPIO:0001946 + CF-T method + + + + + + + + + Chromatin immunoprecipitation + NCBI SRA: ChIP + DPBO + GENEPIO:0001947 + ChIP method + + + + + + + + + Deoxyribonuclease (MNase) digestion + NCBI SRA: DNAse + DPBO + GENEPIO:0001948 + DNAse method + + + + + + + + + Hypo-methylated partial restriction digest + NCBI SRA: HMPR + DPBO + GENEPIO:0001949 + HMPR method + + + + + + + + + Selection by hybridization in array or solution. + NCBI SRA: Hybrid Selection + DPBO + GENEPIO:0001950 + Hybrid Selection method + + + + + + + + + Enrichment by methyl-CpG binding domain. + NCBI SRA: MBD2 protein methyl-CpG binding domain + DPBO + GENEPIO:0001951 + MBD2 protein methyl-CpG binding domain method + + + + + + + + + Methyl Filtrated + NCBI SRA: MF + DPBO + GENEPIO:0001952 + MF method + + + + + + + + + Micrococcal Nuclease (MNase) digestion + NCBI SRA: MNase + DPBO + GENEPIO:0001953 + MNase method + + + + + + + + + Methylation Spanning Linking Library + NCBI SRA: MSLL + DPBO + GENEPIO:0001954 + MSLL method + + + + + + + + + Source material was selected by designed primers. + NCBI SRA: PCR + DPBO + GENEPIO:0001955 + PCR method + + + + + + + + + Rapid Amplification of cDNA Ends. + NCBI SRA: RACE + DPBO + GENEPIO:0001956 + RACE method + + + + + + + + + Source material was selected by randomly generated primers. + NCBI SRA: RANDOM PCR + DPBO + GENEPIO:0001957 + RANDOM PCR method + + + + + + + + + Random selection by shearing or other method. + NCBI SRA: RANDOM + DPBO + GENEPIO:0001958 + RANDOM method + + + + + + + + + Source material was selected by reverse transcription PCR + NCBI SRA: RT-PCR + DPBO + GENEPIO:0001959 + RT-PCR method + + + + + + + + + Reproducible genomic subsets, often generated by restriction fragment size selection, containing a manageable number of loci to facilitate re-sampling. + NCBI SRA: Reduced Representation + DPBO + GENEPIO:0001960 + Reduced Representation method + + + + + + + + + DNA fractionation using restriction enzymes. + NCBI SRA: Restriction Digest + DPBO + GENEPIO:0001961 + Restriction Digest method + + + + + + + + + PolyA selection or enrichment for messenger RNA (mRNA). complementary DNA. + NCBI SRA: cDNA + DPBO + GENEPIO:0001962 + cDNA method + + + + + + + + + Physical selection of size appropriate targets. + NCBI SRA: size fractionation + DPBO + GENEPIO:0001963 + size fractionation method + + + + + + + + + Other library enrichment, screening, or selection process. + NCBI SRA: other + DPBO + GENEPIO:0001964 + other library method @@ -7230,10 +7536,10 @@ - The library source specifies the type of source material that is being sequenced. - DPBO - GENEPIO:0001965 - library source + The library source specifies the type of source material that is being sequenced. + DPBO + GENEPIO:0001965 + library source @@ -7242,12 +7548,12 @@ - Sequencing technique intended for this library. - Damion Dooley - https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly - DPBO - GENEPIO:0001973 - library strategy + Sequencing technique intended for this library. + Damion Dooley + https://www.ncbi.nlm.nih.gov/books/NBK54984/table/SRA_Glossary_BK.T._library_descriptor_te/?report=objectonly + DPBO + GENEPIO:0001973 + library strategy @@ -7255,11 +7561,11 @@ - - A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an 'SQ Module' to support microfluidics. - DPBO - GENEPIO:0100109 - Illumina HiScanSQ + + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry, and contains a HiScan Reader for sequencing and microarray-based analyses as well as an 'SQ Module' to support microfluidics. + DPBO + GENEPIO:0100109 + Illumina HiScanSQ @@ -7267,11 +7573,11 @@ - - A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. - DPBO - GENEPIO:0100112 - Illumina HiSeq X Five + + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that consists of a set of 5 HiSeq X Sequencing Systems. + DPBO + GENEPIO:0100112 + Illumina HiSeq X Five @@ -7279,11 +7585,11 @@ - - A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - DPBO - GENEPIO:0100113 - Illumina HiSeq X Ten + + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + DPBO + GENEPIO:0100113 + Illumina HiSeq X Ten @@ -7291,11 +7597,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. - DPBO - GENEPIO:0100115 - Illumina HiSeq 1500 + + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35-50 Gb per day. + DPBO + GENEPIO:0100115 + Illumina HiSeq 1500 @@ -7303,11 +7609,11 @@ - - A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. - DPBO - GENEPIO:0100121 - Illumina iSeq 100 + + A DNA sequencer manufactured by the Illumina corporation using sequence-by-synthesis chemistry that is lightweight and has an output capacity between 144MB-1.2GB. + DPBO + GENEPIO:0100121 + Illumina iSeq 100 @@ -7315,11 +7621,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - DPBO - GENEPIO:0100123 - Illumina NovaSeq 6000 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + DPBO + GENEPIO:0100123 + Illumina NovaSeq 6000 @@ -7327,11 +7633,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. - DPBO - GENEPIO:0100124 - Illumina MiniSeq + + A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and has an output capacity of 1.65-7.5 Gb. + DPBO + GENEPIO:0100124 + Illumina MiniSeq @@ -7339,11 +7645,11 @@ - - A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. - DPBO - GENEPIO:0100128 - Illumina NextSeq 550 + + A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The 550 is an upgrade on the 500 model. + DPBO + GENEPIO:0100128 + Illumina NextSeq 550 @@ -7351,11 +7657,11 @@ - - A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes 'SMRT Cells' for single-molecule real-time sequencing. The RS was the first model made by the company. - DPBO - GENEPIO:0100131 - PacBio RS + + A DNA sequencer manufactured by the Pacific Biosciences corporation which utilizes 'SMRT Cells' for single-molecule real-time sequencing. The RS was the first model made by the company. + DPBO + GENEPIO:0100131 + PacBio RS @@ -7363,11 +7669,11 @@ - - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - DPBO - GENEPIO:0100133 - PacBio Sequel + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + DPBO + GENEPIO:0100133 + PacBio Sequel @@ -7375,11 +7681,11 @@ - - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. - DPBO - GENEPIO:0100134 - PacBio Sequel II + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. + DPBO + GENEPIO:0100134 + PacBio Sequel II @@ -7387,11 +7693,11 @@ - - A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. - DPBO - GENEPIO:0100136 - Ion Torrent PGM + + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of 300 MB - 1GB. + DPBO + GENEPIO:0100136 + Ion Torrent PGM @@ -7399,11 +7705,11 @@ - - A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. - DPBO - GENEPIO:0100137 - Ion Torrent Proton + + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and has an output capacity of up to 15 Gb. + DPBO + GENEPIO:0100137 + Ion Torrent Proton @@ -7411,11 +7717,11 @@ - - A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. - DPBO - GENEPIO:0100138 - Ion Torrent S5 XL + + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material while producing data faster than the S5 model. + DPBO + GENEPIO:0100138 + Ion Torrent S5 XL @@ -7423,11 +7729,11 @@ - - A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. - DPBO - GENEPIO:0100139 - Ion Torrent S5 + + A DNA sequencer manufactured by the Ion Torrent corporation which utilizes Ion semiconductor sequencing and requires only a small amount of input material. + DPBO + GENEPIO:0100139 + Ion Torrent S5 @@ -7435,11 +7741,11 @@ - - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual - DPBO - GENEPIO:0100141 - Oxford Nanopore GridION + + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, that can run and analyze up to five individual flow cells producing up to 150 Gb of data per run. The sequencer produces real-time results and utilizes nanopore technology with the option of running the flow cells concurrently or individual + DPBO + GENEPIO:0100141 + Oxford Nanopore GridION @@ -7447,11 +7753,11 @@ - - A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - DPBO - GENEPIO:0100142 - Oxford Nanopore MinION + + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + DPBO + GENEPIO:0100142 + Oxford Nanopore MinION @@ -7459,11 +7765,11 @@ - - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - DPBO - GENEPIO:0100143 - Oxford Nanopore PromethION + + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + DPBO + GENEPIO:0100143 + Oxford Nanopore PromethION @@ -7471,11 +7777,11 @@ - - A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'. - DPBO - GENEPIO:0100145 - BGI Genomics BGISEQ-500 + + A DNA sequencer manufactured by the BGI Genomics corporation that utilizes Probe-Anchor Synthesis (cPAS) chemistry and 'DNA Nanoballs'. + DPBO + GENEPIO:0100145 + BGI Genomics BGISEQ-500 @@ -7483,11 +7789,11 @@ - - A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. - DPBO - GENEPIO:0100147 - MGI DNBSEQ-T7 + + A high throughput DNA sequencer manufactured by the MGI corporation with an output capacity of 1; 6TB of data per day. + DPBO + GENEPIO:0100147 + MGI DNBSEQ-T7 @@ -7495,11 +7801,11 @@ - - A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. - DPBO - GENEPIO:0100148 - MGI DNBSEQ-G400 + + A DNA sequencer manufactured by the MGI corporation with an output capacity of 55GB; 1440GB per run. + DPBO + GENEPIO:0100148 + MGI DNBSEQ-G400 @@ -7507,11 +7813,11 @@ - - A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. - DPBO - GENEPIO:0100150 - MGI DNBSEQ-G50 + + A DNA sequencer manufactured by the MGI corporation with an output capacity of 10～150 GB per run and enables different read lengths. + DPBO + GENEPIO:0100150 + MGI DNBSEQ-G50 @@ -7519,10 +7825,10 @@ - A sequence data which is the short name of a gene typically derived from the gene name. - DPBO - GENEPIO:0100598 - gene symbol + A sequence data which is the short name of a gene typically derived from the gene name. + DPBO + GENEPIO:0100598 + gene symbol @@ -7530,9 +7836,9 @@ - DPBO - GEO:000000370 - geographical entity + DPBO + GEO:000000370 + geographical entity @@ -7541,14 +7847,14 @@ - A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. - François Modave - Mathias Brochhausen - Matt Diller - William R. Hogan - DPBO - GEO:000000372 - geographical region + A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. + François Modave + Mathias Brochhausen + Matt Diller + William R. Hogan + DPBO + GEO:000000372 + geographical region @@ -7556,9 +7862,9 @@ - DPBO - MIAPPE:0049 - Biological material preprocessing + DPBO + MIAPPE:0049 + Biological material preprocessing @@ -7566,9 +7872,9 @@ - DPBO - MIAPPE:0095 - Growth facility + DPBO + MIAPPE:0095 + Growth facility @@ -7576,10 +7882,10 @@ - Reference of a protein object pointing to its genomic or nucleic acid sequence. - DPBO - MI:0251 - gene product + Reference of a protein object pointing to its genomic or nucleic acid sequence. + DPBO + MI:0251 + gene product @@ -7587,16 +7893,16 @@ - Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. - DPBO - MI:0507 - tag + Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. + DPBO + MI:0507 + tag - Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. - PMID:14755292 + Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule. + PMID:14755292 @@ -7604,9 +7910,9 @@ - DPBO - NCIT:C126370 - Cover Slip + DPBO + NCIT:C126370 + Cover Slip @@ -7614,11 +7920,11 @@ - - A proprietary next-generation DNA sequencing system from BGI Genomics using combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB) technology. The cPAS chemistry works by incorporating a fluorescent probe to a DNA anchor on the DNB, followed by high-resolution digital imaging. - DPBO - NCIT:C146812 - BGISEQ-500 Sequencing + + A proprietary next-generation DNA sequencing system from BGI Genomics using combinatorial Probe-Anchor Synthesis (cPAS) and improved DNA Nanoballs (DNB) technology. The cPAS chemistry works by incorporating a fluorescent probe to a DNA anchor on the DNB, followed by high-resolution digital imaging. + DPBO + NCIT:C146812 + BGISEQ-500 Sequencing @@ -7626,11 +7932,11 @@ - - A next-generation DNA sequencing service offered by Complete Genomics. Unamplified human genomic DNA is sheared into 500bp fragments and then amplified to create DNA nano-balls (DNBs). The DNBs are arrayed on a substrate and their sequence is determined by Combinatorial Probe-Anchor Ligation (cPAL) sequencing. - DPBO - NCIT:C146815 - Complete Genomics Sequencing + + A next-generation DNA sequencing service offered by Complete Genomics. Unamplified human genomic DNA is sheared into 500bp fragments and then amplified to create DNA nano-balls (DNBs). The DNBs are arrayed on a substrate and their sequence is determined by Combinatorial Probe-Anchor Ligation (cPAL) sequencing. + DPBO + NCIT:C146815 + Complete Genomics Sequencing @@ -7638,16 +7944,16 @@ - The name of the software program capture and/or process imaging data. - DPBO - NCIT:C175898 - Imaging Software Name + The name of the software program capture and/or process imaging data. + DPBO + NCIT:C175898 + Imaging Software Name - The name of the software program capture and/or process imaging data. - NCI + The name of the software program capture and/or process imaging data. + NCI @@ -7655,9 +7961,9 @@ - DPBO - NCIT:C181919 - Objective Lens + DPBO + NCIT:C181919 + Objective Lens @@ -7665,11 +7971,11 @@ - MIAPPE:0043 - NCBITaxon:species - DPBO - NCIT:C45293 - Species + MIAPPE:0043 + NCBITaxon:species + DPBO + NCIT:C45293 + Species @@ -7677,11 +7983,11 @@ - - RNA present in the cytoplasm. It is involved in the protein export process from the cells. - DPBO - NCIT:C84512 - Cytoplasmic RNA + + RNA present in the cytoplasm. It is involved in the protein export process from the cells. + DPBO + NCIT:C84512 + Cytoplasmic RNA @@ -7690,9 +7996,9 @@ - DPBO - NMR:1000019 - sample pH + DPBO + NMR:1000019 + sample pH @@ -7700,10 +8006,10 @@ - Parameters used in the NMR spectrometry acquisition. - DPBO - NMR:1001954 - NMR acquisition parameter + Parameters used in the NMR spectrometry acquisition. + DPBO + NMR:1001954 + NMR acquisition parameter @@ -7711,9 +8017,9 @@ - DPBO - NMR:1002011 - pH + DPBO + NMR:1002011 + pH @@ -7721,10 +8027,10 @@ - The intensity of an electric, magnetic, or other field. - DPBO - NMR:1400027 - field strength + The intensity of an electric, magnetic, or other field. + DPBO + NMR:1400027 + field strength @@ -7733,10 +8039,10 @@ - The number of repeat scans performed and summed to create the data set for an NMR sample. - DPBO - NMR:1400087 - number of scans + The number of repeat scans performed and summed to create the data set for an NMR sample. + DPBO + NMR:1400087 + number of scans @@ -7745,10 +8051,10 @@ - DPBO - NMR:1400253 - defneed - magnetic field strength + DPBO + NMR:1400253 + defneed + magnetic field strength @@ -7756,10 +8062,10 @@ - a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. - DPBO - OBI:0000079 - culture medium + a processed material that provides the needed nourishment for microorganisms or cells grown in vitro. + DPBO + OBI:0000079 + culture medium @@ -7767,10 +8073,10 @@ - A planned process which results in physical changes in a specified input material - DPBO - OBI:0000094 - material processing + A planned process which results in physical changes in a specified input material + DPBO + OBI:0000094 + material processing @@ -7778,11 +8084,11 @@ - - Is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. - DPBO - OBI:0000702 - 454 Genome Sequencer FLX + + Is a DNA sequencer which was first manufactured by 454 Life Science Corporation in 2008 and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information. It has the ability to sequence 400-600 million base pairs per run with 400-500 base pair read lengths. + DPBO + OBI:0000702 + 454 Genome Sequencer FLX @@ -7790,11 +8096,11 @@ - - Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry - DPBO - OBI:0000717 - HeliScope Single Molecule Sequencer + + Is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry + DPBO + OBI:0000717 + HeliScope Single Molecule Sequencer @@ -7802,9 +8108,9 @@ - DPBO - OBI:0000967 - container + DPBO + OBI:0000967 + container @@ -7812,10 +8118,10 @@ - An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. - DPBO - OBI:0001048 - digital camera + An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor. + DPBO + OBI:0001048 + digital camera @@ -7823,11 +8129,11 @@ - - An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. - DPBO - OBI:0002000 - Genome Analyzer IIx + + An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications. + DPBO + OBI:0002000 + Genome Analyzer IIx @@ -7835,11 +8141,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. - DPBO - OBI:0002001 - Illumina HiSeq 2000 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 55 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for multiple samples in a single run. + DPBO + OBI:0002001 + Illumina HiSeq 2000 @@ -7847,11 +8153,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. - DPBO - OBI:0002002 - Illumina HiSeq 2500 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and a throughput of up to 160 Gb per day. Built upon sequencing by synthesis technology, the machine is optimized for generation of data for batching multiple samples or rapid results on a few samples. + DPBO + OBI:0002002 + Illumina HiSeq 2500 @@ -7859,11 +8165,11 @@ - - A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. - DPBO - OBI:0002007 - SOLiD 3 Plus System + + A DNA sequencer which is manufacted by the Applied Biosystems corporation. Built upon SOLiD sequencing technology, the machine generates greater than 1 billion mappable reads per run. + DPBO + OBI:0002007 + SOLiD 3 Plus System @@ -7871,11 +8177,11 @@ - - A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. - DPBO - OBI:0002012 - PacBio RS II + + A DNA sequencer which is manufactured by the Pacific Biosciences corporation. Built upon single molecule real-time sequencing technology, the machine is optimized for generation with long reads and high consensus accuracy. + DPBO + OBI:0002012 + PacBio RS II @@ -7883,11 +8189,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. - DPBO - OBI:0002022 - Illumina HiSeq 1000 + + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell and a throughput of up to 35 Gb per day. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. + DPBO + OBI:0002022 + Illumina HiSeq 1000 @@ -7895,11 +8201,11 @@ - - A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. - DPBO - OBI:0002048 - Illumina HiSeq 3000 + + A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day. + DPBO + OBI:0002048 + Illumina HiSeq 3000 @@ -7907,11 +8213,11 @@ - - A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. - DPBO - OBI:0002049 - Illumina HiSeq 4000 + + A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day. + DPBO + OBI:0002049 + Illumina HiSeq 4000 @@ -7919,11 +8225,11 @@ - - A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. - DPBO - OBI:0002129 - Illumina HiSeq X Ten + + A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems. + DPBO + OBI:0002129 + Illumina HiSeq X Ten @@ -7931,11 +8237,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. - DPBO - OBI:0002630 - Illumina NovaSeq 6000 + + A DNA sequencer which is manufactured by the Illumina corporation, with two flow cells and an output of up to 6000 Gb (32-40 B reads per run). The sequencer utilizes synthesis technology and patterned flow cells to optimize throughput and even spacing of sequencing clusters. + DPBO + OBI:0002630 + Illumina NovaSeq 6000 @@ -7943,11 +8249,11 @@ - - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation - DPBO - OBI:0002632 - PacBio Sequel + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation with long reads and high consensus accuracy, and manufactured by the Pacific Biosciences corporation + DPBO + OBI:0002632 + PacBio Sequel @@ -7955,11 +8261,11 @@ - - A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. - DPBO - OBI:0002633 - PacBio Sequel II + + A DNA sequencer built upon single molecule real-time sequencing technology, optimized for generation of highly accurate ('HiFi') long reads, and which is manufactured by the Pacific Biosciences corporation. + DPBO + OBI:0002633 + PacBio Sequel II @@ -7967,11 +8273,11 @@ - - A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. - DPBO - OBI:0002750 - Oxford Nanopore MinION + + A portable DNA sequencer which is manufactured by the Oxford Nanopore Technologies corporation, that uses consumable flow cells producing up to 30 Gb of DNA sequence data per flow cell. The sequencer produces real-time results and utilizes nanopore technology with up to 512 nanopore channels in the sensor array. + DPBO + OBI:0002750 + Oxford Nanopore MinION @@ -7979,11 +8285,11 @@ - - A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. - DPBO - OBI:0002752 - Oxford Nanopore PromethION + + A DNA sequencer that is manufactured by the Oxford Nanopore Technologies corporation, capable of running up to 48 flow cells and producing up to 7.6 Tb of data per run. The sequencer produces real-time results and utilizes Nanopore technology, with each flow cell allowing up to 3,000 nanopores to be sequencing simultaneously. + DPBO + OBI:0002752 + Oxford Nanopore PromethION @@ -7991,11 +8297,11 @@ - - A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. - DPBO - OBI:0003114 - Illumina MiniSeq + + A small benchtop DNA sequencer which is manufactured by the Illumina corporation with integrated cluster generation, sequencing and data analysis. The sequencer accommodates various flow cell configurations and can produce up to 25M single reads or 50M paired-end reads per run. + DPBO + OBI:0003114 + Illumina MiniSeq @@ -8003,11 +8309,11 @@ - - A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. - DPBO - OBI:0003386 - Illumina HiSeq 1500 + + A DNA sequencer which is manufactured by the Illumina corporation, with a single flow cell. Built upon sequencing by synthesis technology, the machine employs dual surface imaging and offers two high-output options and one rapid-run option. + DPBO + OBI:0003386 + Illumina HiSeq 1500 @@ -8015,13 +8321,13 @@ - A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. - MIAPPE:0041 - NCIT:C14250 - NFDI4PSO:0000030 - DPBO - OBI:0100026 - organism + A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. + MIAPPE:0041 + NCIT:C14250 + NFDI4PSO:0000030 + DPBO + OBI:0100026 + organism @@ -8029,10 +8335,10 @@ - A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) - DPBO - OBI:0400169 - microscope + A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) + DPBO + OBI:0400169 + microscope @@ -8040,10 +8346,10 @@ - A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument - DPBO - OBI:0400170 - microscope slide + A microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument + DPBO + OBI:0400170 + microscope slide @@ -8051,11 +8357,11 @@ - - DPBO - OME:Objective - Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective - obsolete_Objective + + DPBO + OME:Objective + Class "Objective" is microscopes' objective lens. 19.02.2024: term has been deprecated, please use REPR:Objective + obsolete_Objective true @@ -8064,9 +8370,9 @@ - DPBO - PATO:0000918 - volume + DPBO + PATO:0000918 + volume @@ -8074,17 +8380,17 @@ - The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. - DPBO - PATO:0015031 - contamination + The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. + DPBO + PATO:0015031 + contamination - The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. - https://en.wikipedia.org/wiki/Contamination - https://github.com/pato-ontology/pato/issues/420 + The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. + https://en.wikipedia.org/wiki/Contamination + https://github.com/pato-ontology/pato/issues/420 @@ -8093,10 +8399,10 @@ - A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof. - DPBO - PECO:0001001 - plant exposure + A plant experimental condition (PECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (biotic plant exposurePECO:0007359) or set of conditions describing the application of an abiotic (PECO:0007191) or biotic plant exposure (PECO:0007357plant experimental condition) or set of conditions describing the application of an abiotic (abiotic plant exposure) or biotic plant exposure (PECO:0007357) or the combinatorial application thereof. + DPBO + PECO:0001001 + plant exposure @@ -8104,10 +8410,10 @@ - - DPBO - PO:0009001 - fruit + + DPBO + PO:0009001 + fruit @@ -8115,10 +8421,10 @@ - - DPBO - PO:0009008 - plant organ + + DPBO + PO:0009008 + plant organ @@ -8126,10 +8432,10 @@ - - DPBO - PO:0009010 - seed + + DPBO + PO:0009010 + seed @@ -8137,10 +8443,10 @@ - - DPBO - PO:0025498 - cardinal part of multi-tissue plant structure + + DPBO + PO:0025498 + cardinal part of multi-tissue plant structure @@ -8148,12 +8454,12 @@ - jg - 2011-07-22T09:15:33Z - PRIDE - PRIDE:0000307 - Defines various quantification methods - Quantification method + jg + 2011-07-22T09:15:33Z + PRIDE + PRIDE:0000307 + Defines various quantification methods + Quantification method @@ -8162,12 +8468,12 @@ - jg - 2011-07-22T09:16:24Z - PRIDE - PRIDE:0000308 - Describes gel-based quantification methods - Gel-based quantification method + jg + 2011-07-22T09:16:24Z + PRIDE + PRIDE:0000308 + Describes gel-based quantification methods + Gel-based quantification method @@ -8176,12 +8482,12 @@ - jg - 2011-07-22T09:17:03Z - PRIDE - PRIDE:0000309 - Describes gel-free quantification methods - Gel-free quantification method + jg + 2011-07-22T09:17:03Z + PRIDE + PRIDE:0000309 + Describes gel-free quantification methods + Gel-free quantification method @@ -8190,12 +8496,12 @@ - jg - 2011-07-22T09:17:34Z - PRIDE - PRIDE:0000310 - Describes quantification techniques using isotope labeling - Isotope labeling + jg + 2011-07-22T09:17:34Z + PRIDE + PRIDE:0000310 + Describes quantification techniques using isotope labeling + Isotope labeling @@ -8204,12 +8510,12 @@ - jg - 2011-07-22T09:18:39Z - PRIDE - PRIDE:0000311 - Describes quantification techniques based on selected / multiple reaction monitoring - Selected Reaction Monitoring + jg + 2011-07-22T09:18:39Z + PRIDE + PRIDE:0000311 + Describes quantification techniques based on selected / multiple reaction monitoring + Selected Reaction Monitoring @@ -8218,12 +8524,12 @@ - jg - 2011-07-22T09:19:54Z - PRIDE - PRIDE:0000312 - Describes label free quantification techniques. - Label free + jg + 2011-07-22T09:19:54Z + PRIDE + PRIDE:0000312 + Describes label free quantification techniques. + Label free @@ -8232,12 +8538,12 @@ - jg - 2011-07-22T09:20:23Z - PRIDE - PRIDE:0000313 - Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level - iTRAQ + jg + 2011-07-22T09:20:23Z + PRIDE + PRIDE:0000313 + Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level + iTRAQ @@ -8246,13 +8552,13 @@ - jg - 2011-07-22T09:23:12Z - Tandem Mass Tag - PRIDE - PRIDE:0000314 - Tandem Mass Tag is a MS2 based isotope labeling quantification technique - TMT + jg + 2011-07-22T09:23:12Z + Tandem Mass Tag + PRIDE + PRIDE:0000314 + Tandem Mass Tag is a MS2 based isotope labeling quantification technique + TMT @@ -8261,13 +8567,13 @@ - jg - 2011-07-22T09:25:50Z - Stable isotope labeling with amino acids in cell culture - PRIDE - PRIDE:0000315 - Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification - SILAC + jg + 2011-07-22T09:25:50Z + Stable isotope labeling with amino acids in cell culture + PRIDE + PRIDE:0000315 + Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification + SILAC @@ -8276,12 +8582,12 @@ - jg - 2011-07-22T09:28:05Z - PRIDE - PRIDE:0000316 - Describes isotope labeling quantification techniques detectable at MS1 level. - MS1 based isotope labeling + jg + 2011-07-22T09:28:05Z + PRIDE + PRIDE:0000316 + Describes isotope labeling quantification techniques detectable at MS1 level. + MS1 based isotope labeling @@ -8290,12 +8596,12 @@ - jg - 2011-07-22T09:29:15Z - PRIDE - PRIDE:0000317 - Describes isotope labeling quantification techniques detectable at MS1 level. - MS2 based isotope labeling + jg + 2011-07-22T09:29:15Z + PRIDE + PRIDE:0000317 + Describes isotope labeling quantification techniques detectable at MS1 level. + MS2 based isotope labeling @@ -8304,12 +8610,12 @@ - jg - 2011-07-22T09:30:12Z - PRIDE - PRIDE:0000318 - The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. - 18O + jg + 2011-07-22T09:30:12Z + PRIDE + PRIDE:0000318 + The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen. + 18O @@ -8318,13 +8624,13 @@ - jg - 2011-07-22T09:31:24Z - Isotope-Coded Affinity Tags - PRIDE - PRIDE:0000319 - Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. - ICAT + jg + 2011-07-22T09:31:24Z + Isotope-Coded Affinity Tags + PRIDE + PRIDE:0000319 + Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements. + ICAT @@ -8333,12 +8639,12 @@ - jg - 2011-07-22T09:32:46Z - PRIDE - PRIDE:0000320 - AQUA is an isotope labeling based quantification technique that uses known peptides. - AQUA + jg + 2011-07-22T09:32:46Z + PRIDE + PRIDE:0000320 + AQUA is an isotope labeling based quantification technique that uses known peptides. + AQUA @@ -8347,13 +8653,13 @@ - jg - 2011-07-22T09:34:37Z - Isotope-coded protein label - PRIDE - PRIDE:0000321 - Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. - ICPL + jg + 2011-07-22T09:34:37Z + Isotope-coded protein label + PRIDE + PRIDE:0000321 + Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses. + ICPL @@ -8362,13 +8668,13 @@ - jg - 2011-07-22T09:36:57Z - Exponentially Modified Protein Abundance Index - PRIDE - PRIDE:0000322 - The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result. - emPAI + jg + 2011-07-22T09:36:57Z + Exponentially Modified Protein Abundance Index + PRIDE + PRIDE:0000322 + The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result. + emPAI @@ -8377,13 +8683,13 @@ - jg - 2011-07-22T09:38:17Z - Total Ion Current - PRIDE - PRIDE:0000323 - The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. - TIC + jg + 2011-07-22T09:38:17Z + Total Ion Current + PRIDE + PRIDE:0000323 + The Total Ion Current (TIC) can be measured or calculated in order to target specific ions. + TIC @@ -8392,10 +8698,10 @@ - rw - PRIDE - PRIDE:0000425 - MS1 intensity based label-free quantification method + rw + PRIDE + PRIDE:0000425 + MS1 intensity based label-free quantification method @@ -8404,11 +8710,11 @@ - acsordas - PRIDE - PRIDE:0000435 - Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140. - Peptide counting + acsordas + PRIDE + PRIDE:0000435 + Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140. + Peptide counting @@ -8417,11 +8723,11 @@ - acsordas - PRIDE - PRIDE:0000436 - Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 - Spectrum counting + acsordas + PRIDE + PRIDE:0000436 + Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140 + Spectrum counting @@ -8430,11 +8736,11 @@ - acsordas - PRIDE - PRIDE:0000437 - Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 - Protein Abundance Index - PAI + acsordas + PRIDE + PRIDE:0000437 + Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140 + Protein Abundance Index - PAI @@ -8443,11 +8749,11 @@ - acsordas - PRIDE - PRIDE:0000438 - Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 - Spectrum count/molecular weight + acsordas + PRIDE + PRIDE:0000438 + Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140 + Spectrum count/molecular weight @@ -8456,11 +8762,11 @@ - acsordas - PRIDE - PRIDE:0000439 - The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 - Spectral Abundance Factor - SAF + acsordas + PRIDE + PRIDE:0000439 + The spectrum count is normalized for protein length. Method reviewed in PMID 22772140 + Spectral Abundance Factor - SAF @@ -8469,11 +8775,11 @@ - acsordas - PRIDE - PRIDE:0000440 - Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 - Normalized Spectral Abundance Factor - NSAF + acsordas + PRIDE + PRIDE:0000440 + Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140 + Normalized Spectral Abundance Factor - NSAF @@ -8482,11 +8788,11 @@ - acsordas - PRIDE - PRIDE:0000441 - Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 - APEX - Absolute Protein Expression + acsordas + PRIDE + PRIDE:0000441 + Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140 + APEX - Absolute Protein Expression @@ -8494,10 +8800,10 @@ - Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method. - DPBO - PRIDE:0000457 - Experiment Type + Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method. + DPBO + PRIDE:0000457 + Experiment Type @@ -8506,16 +8812,16 @@ - Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. - PRIDE - PRIDE:0000463 - Parallel Reaction Monitoring (PRM) + Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. + PRIDE + PRIDE:0000463 + Parallel Reaction Monitoring (PRM) - Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. - PRIDE:PRIDE + Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis. + PRIDE:PRIDE @@ -8524,18 +8830,18 @@ - Dimethyl Labeling (DML) - yperez - 2019-08-07T15:21:19Z - PRIDE - PRIDE:0000513 - Dimethyl Labeling + Dimethyl Labeling (DML) + yperez + 2019-08-07T15:21:19Z + PRIDE + PRIDE:0000513 + Dimethyl Labeling - Dimethyl Labeling (DML) - PRIDE:PRIDE + Dimethyl Labeling (DML) + PRIDE:PRIDE @@ -8543,17 +8849,17 @@ - Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 - yperez - DPBO - PRIDE:0000650 - diaPASEF + Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 + yperez + DPBO + PRIDE:0000650 + diaPASEF - Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 - PRIDE:PRIDE + Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825 + PRIDE:PRIDE @@ -8561,10 +8867,10 @@ - A biotic plant stress caused by exposure to an environment containing a biological stress agent. - DPBO - PSO:0000013 - plant disease + A biotic plant stress caused by exposure to an environment containing a biological stress agent. + DPBO + PSO:0000013 + plant disease @@ -8572,10 +8878,10 @@ - The microscope's objective lens. - DPBO - REPR:Objective - Objective + The microscope's objective lens. + DPBO + REPR:Objective + Objective @@ -8583,10 +8889,10 @@ - A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. - DPBO - REPR:Well - Well + A Well is a component of the Well/Plate/Screen construct to describe screening applications. A Well has a number of WellSample elements that link to the Images collected in this well. + DPBO + REPR:Well + Well @@ -8594,9 +8900,9 @@ - DPBO - SCTID:71661000 - cover slip preparation (procedure) + DPBO + SCTID:71661000 + cover slip preparation (procedure) @@ -8604,10 +8910,10 @@ - Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point. - DPBO - SIO:000318 - longitude + Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point. + DPBO + SIO:000318 + longitude @@ -8615,10 +8921,10 @@ - Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane - DPBO - SIO:000319 - latitude + Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane + DPBO + SIO:000319 + latitude @@ -8626,10 +8932,10 @@ - data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making - DPBO - SIO:001051 - data analysis + data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making + DPBO + SIO:001051 + data analysis @@ -8637,10 +8943,10 @@ - A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid. - DPBO - SIO:010016 - nucleic acid sequence + A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid. + DPBO + SIO:010016 + nucleic acid sequence @@ -8648,9 +8954,9 @@ - DPBO - SNOMED:430862008 - Microscope slide mounting medium (substance) + DPBO + SNOMED:430862008 + Microscope slide mounting medium (substance) @@ -8658,27 +8964,27 @@ - The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. - INSDC_feature:regulatory - http://en.wikipedia.org/wiki/Terminator_(genetics) - INSDC_qualifier:terminator - terminator sequence - DPBO - SO:0000141 - Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. - terminator + The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. + INSDC_feature:regulatory + http://en.wikipedia.org/wiki/Terminator_(genetics) + INSDC_qualifier:terminator + terminator sequence + DPBO + SO:0000141 + Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. + terminator - The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. - http://www.insdc.org/files/feature_table.html + The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. + http://www.insdc.org/files/feature_table.html - http://en.wikipedia.org/wiki/Terminator_(genetics) - wiki + http://en.wikipedia.org/wiki/Terminator_(genetics) + wiki @@ -8686,10 +8992,10 @@ - A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription. - DPBO - SO:0000167 - promoter + A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription. + DPBO + SO:0000167 + promoter @@ -8698,19 +9004,19 @@ - The first base to be translated into protein. - coding start - translation initiation site - sequence - translation start - SO:0000323 - coding_start + The first base to be translated into protein. + coding start + translation initiation site + sequence + translation start + SO:0000323 + coding_start - The first base to be translated into protein. - SO:ke + The first base to be translated into protein. + SO:ke @@ -8719,19 +9025,19 @@ - The last base to be translated into protein. It does not include the stop codon. - coding end - translation termination site - translation_end - sequence - SO:0000327 - coding_end + The last base to be translated into protein. It does not include the stop codon. + coding end + translation termination site + translation_end + sequence + SO:0000327 + coding_end - The last base to be translated into protein. It does not include the stop codon. - SO:ke + The last base to be translated into protein. It does not include the stop codon. + SO:ke @@ -8740,19 +9046,19 @@ - A promoter that can allow for transcription in both directions. - bidirectional promoter - sequence - SO:0000568 - Definition updated in Aug 2020 by Dave Sant. - bidirectional_promoter + A promoter that can allow for transcription in both directions. + bidirectional promoter + sequence + SO:0000568 + Definition updated in Aug 2020 by Dave Sant. + bidirectional_promoter - A promoter that can allow for transcription in both directions. - PMID:21601935 - SO:ke + A promoter that can allow for transcription in both directions. + PMID:21601935 + SO:ke @@ -8760,10 +9066,10 @@ - A region of a CDS. - DPBO - SO:0000851 - CDS_region + A region of a CDS. + DPBO + SO:0000851 + CDS_region @@ -8771,12 +9077,12 @@ - - Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. - DPBO:0000035 - DPBO - SWO:1100130 - Seurat + + Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. + DPBO:0000035 + DPBO + SWO:1100130 + Seurat @@ -8784,9 +9090,9 @@ - DPBO - UO:0000000 - unit + DPBO + UO:0000000 + unit @@ -8795,18 +9101,18 @@ - A unit which is a standard measure of the rate of change of velocity in either speed or direction. - george gkoutos - unit.ontology - UO:0000048 - - acceleration unit + A unit which is a standard measure of the rate of change of velocity in either speed or direction. + george gkoutos + unit.ontology + UO:0000048 + + acceleration unit - A unit which is a standard measure of the rate of change of velocity in either speed or direction. - Wikipedia:Wikipedia + A unit which is a standard measure of the rate of change of velocity in either speed or direction. + Wikipedia:Wikipedia @@ -8814,9 +9120,9 @@ - DPBO - UO:0010006 - ratio + DPBO + UO:0010006 + ratio @@ -8824,9 +9130,9 @@ - DPBO - data:0962 - Small molecule report + DPBO + data:0962 + Small molecule report @@ -8834,9 +9140,9 @@ - DPBO - data:0982 - Molecule identifier + DPBO + data:0982 + Molecule identifier @@ -8844,9 +9150,9 @@ - DPBO - data:0984 - Molecule name + DPBO + data:0984 + Molecule name @@ -8856,15 +9162,15 @@ - Unique name of a chemical compound. - beta12orEarlier - Chemical name - DPBO - data:0990 - - - - Compound name + Unique name of a chemical compound. + beta12orEarlier + Chemical name + DPBO + data:0990 + + + + Compound name @@ -8879,18 +9185,18 @@ - true - Identifier of an entry from a database of chemicals. - beta12orEarlier - Chemical compound identifier - Compound ID - Small molecule identifier - DPBO - data:1086 - - - - Compound identifier + true + Identifier of an entry from a database of chemicals. + beta12orEarlier + Chemical compound identifier + Compound ID + Small molecule identifier + DPBO + data:1086 + + + + Compound identifier @@ -8898,10 +9204,10 @@ - An identifier of an open reading frame. - DPBO - data:2795 - ORF identifier + An identifier of an open reading frame. + DPBO + data:2795 + ORF identifier @@ -8909,13 +9215,13 @@ - - Sequencing technique intended for a next generation sequencing library. - GENEPIO:0001973 - DPBO - obsolete_DPBO:0000035 - term is redundant, please use GENEPIO:0001973 - library strategy + + Sequencing technique intended for a next generation sequencing library. + GENEPIO:0001973 + DPBO + obsolete_DPBO:0000035 + term is redundant, please use GENEPIO:0001973 + library strategy true @@ -8924,23 +9230,23 @@ - 1.1 - Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. - Oligonucleotide alignment - Oligonucleotide alignment construction - Oligonucleotide alignment generation - Oligonucleotide mapping - Read alignment - Short oligonucleotide alignment - Short read alignment - Short read mapping - Short sequence read mapping - DPBO - operation:3198 - - - The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. - Read mapping + 1.1 + Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. + Oligonucleotide alignment + Oligonucleotide alignment construction + Oligonucleotide alignment generation + Oligonucleotide mapping + Read alignment + Short oligonucleotide alignment + Short read alignment + Short read mapping + Short sequence read mapping + DPBO + operation:3198 + + + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. + Read mapping @@ -8948,9 +9254,9 @@ - DPBO - topic:0077 - Nucleic acids + DPBO + topic:0077 + Nucleic acids @@ -8959,255 +9265,255 @@ - RNA sequences and structures. - beta12orEarlier - RNA + RNA sequences and structures. + beta12orEarlier + RNA - Small RNA - DPBO - topic:0099 - - - RNA + Small RNA + DPBO + topic:0099 + + + RNA - + - - - A mutant in which a gene ore genes are expressed at higher levels than the wild type. - DPBO - MCO_0000041 - overexpression mutant + + + A mutant in which a gene ore genes are expressed at higher levels than the wild type. + DPBO + MCO_0000041 + overexpression mutant - + - - - A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality. - DPBO - MCO_0000042 - gene variant mutant + + + A mutant genotype in which one or more genes can have modifications (subtitutions, indels, partial truncations, etc), but they conserve functionality. + DPBO + MCO_0000042 + gene variant mutant - + - - - A mutant in which the function of a target gene has been disrupted within its normal biological context. Utilized to examine the involvement of a gene in a complex biological process. - DPBO - MCO_0000051 - knockout mutant + + + A mutant in which the function of a target gene has been disrupted within its normal biological context. Utilized to examine the involvement of a gene in a complex biological process. + DPBO + MCO_0000051 + knockout mutant - + - - - a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication. - DPBO - MCO_0000052 - plasmid mutant + + + a mutant in which a foreign DNA sequence is introduced to cell in an extrachromosomal unit of replication. + DPBO + MCO_0000052 + plasmid mutant - + - - - An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit. - DPBO - MCO_0000059 - OD600 + + + An optical density that specifies the amount of light of 600 nm of wavelenght the bearer is able to transmit. + DPBO + MCO_0000059 + OD600 - + - - A physical quality that inheres in a bearer by virtue of the amount of light that the bearer of the quality is able to transmit. - DPBO - MCO_0000077 - optical density + + A physical quality that inheres in a bearer by virtue of the amount of light that the bearer of the quality is able to transmit. + DPBO + MCO_0000077 + optical density - + - - + + - DPBO - MCO_0000173 - nutrient availability stress treatment + DPBO + MCO_0000173 + nutrient availability stress treatment - + - - + + - DPBO - MCO_0000174 - nutrient depletion treatment + DPBO + MCO_0000174 + nutrient depletion treatment - + - - + + - DPBO - MCO_0000177 - iron depletion + DPBO + MCO_0000177 + iron depletion - + - - + + - DPBO - MCO_0000178 - carbon starvation + DPBO + MCO_0000178 + carbon starvation - + - - + + - DPBO - MCO_0000179 - nitrogen starvation + DPBO + MCO_0000179 + nitrogen starvation - + - - + + - DPBO - MCO_0000180 - phosphate starvation + DPBO + MCO_0000180 + phosphate starvation - + - - A biological quality that inheres in specific organisms and that describes its total genetic content - DPBO - MCO_0000851 - genotype + + A biological quality that inheres in specific organisms and that describes its total genetic content + DPBO + MCO_0000851 + genotype - + - - A process in which the act is intended to modify or alter some other material entity. - DPBO - MCO_0000866 - treatment + + A process in which the act is intended to modify or alter some other material entity. + DPBO + MCO_0000866 + treatment - + - - - A proprietary next-generation DNA sequencing system from Solexa that uses reversible terminator nucleotides. The genomic DNA to be sequenced is fragmented and ligated to adapter molecules on both ends to construct an Illumina-specific adapter library. PCR amplification of the DNA fragments is then performed using the adapter sequence as primer. Sequencing is carried out by repeated cycles of adding reversible fluorescent-labelled nucleotide and incorporation of the nucleotides to the complementary strand. The fluorescence of the incorporated nucleotides is detected. - DPBO - NCIT_C146817 - Illumina Sequencing + + + A proprietary next-generation DNA sequencing system from Solexa that uses reversible terminator nucleotides. The genomic DNA to be sequenced is fragmented and ligated to adapter molecules on both ends to construct an Illumina-specific adapter library. PCR amplification of the DNA fragments is then performed using the adapter sequence as primer. Sequencing is carried out by repeated cycles of adding reversible fluorescent-labelled nucleotide and incorporation of the nucleotides to the complementary strand. The fluorescence of the incorporated nucleotides is detected. + DPBO + NCIT_C146817 + Illumina Sequencing - + - - - A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis. - DPBO - NCIT_C146818 - Nanopore Sequencing + + + A proprietary next-generation DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence a DNA molecule as it passes through a nanopore, driven by electrophoresis. + DPBO + NCIT_C146818 + Nanopore Sequencing - + - - - An altered form of an individual, organism, population, or genetic character that differs from the corresponding wild type due to one or more alterations (mutations). - DPBO - NCIT_C25360 - mutant + + + An altered form of an individual, organism, population, or genetic character that differs from the corresponding wild type due to one or more alterations (mutations). + DPBO + NCIT_C25360 + mutant - + - - - The naturally-occurring, normal, non-mutated version of a gene or genome. - DPBO - NCIT_C62195 - wild type + + + The naturally-occurring, normal, non-mutated version of a gene or genome. + DPBO + NCIT_C62195 + wild type - + - - - A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. - DPBO - OBI_0000869 - polyA RNA + + + A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3' end are purified. + DPBO + OBI_0000869 + polyA RNA - + - - DPBO - ObsoleteClass - Obsolete Class + + DPBO + ObsoleteClass + Obsolete Class - +