2018-05-23

This release includes 38 new terms since the 2018-02-12 release.

• OBI:0002457 precision nuclear run-on sequencing assay
• OBI:0002458 chromosome conformation capture-on-chip assay
• OBI:0002459 genotype phasing by Hi-C assay
• OBI:0002460 defined population inclusion criterion
• OBI:0002461 BCL format
• OBI:0002462 ERCC RNA spike-in
• OBI:0002463 SIRV RNA spike-in
• OBI:0002464 SRS identifier
• OBI:0002465 age since culture seeding measurement datum
• OBI:0002466 alignment counting algorithm
• OBI:0002467 alignment counting application
• OBI:0002468 base calling algorithm
• OBI:0002469 base calling application
• OBI:0002470 bcl2fastq software application
• OBI:0002471 date process started
• OBI:0002472 dbGaP study identifier
• OBI:0002473 material amplification role
• OBI:0002474 material sequencing library preparation role
• OBI:0002475 number of PCR cycles during library construction
• OBI:0002476 number of rounds of amplification
• OBI:0002477 reference genome role
• OBI:0002478 reference genome-transcriptome alignment algorithm
• OBI:0002479 sequence read length measurement datum
• OBI:0002480 sequencing library input quantity measurement datum
• OBI:0002481 single-end library
• OBI:0002482 specimen harvest quantity
• OBI:0002483 spike-in dilution factor
• OBI:0002484 star algorithm
• OBI:0002485 transcript analysis by single-end sequencing
• OBI:0002486 verse algorithm
• OBI:0002487 microraft
• OBI:0002488 pipette
• OBI:0002570 nCounter Mouse miRNA Expression array
• OBI:0002571 polyA-selected RNA sequencing assay
• OBI:0002572 polyA-depleted RNA sequencing assay
• OBI:0002573 polyA depleted RNA extract
• OBI:0002574 RNA extraction with polyA depletion
• OBI:0002575 isoform sequencing

2018-02-12

This release includes 13 new terms since the 2017-11-07 release.

• OBI:0002444 measurand role
• OBI:0002445 transcription start site mapping by primer extension assay
• OBI:0002446 proteomic profiling design
• OBI:0002447 suppression subtractive hybridization
• OBI:0002448 differential screening hybridization
• OBI:0002449 footprinting assay measuring binding of a B cell epitope:antibody complex
• OBI:0002450 hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex
• OBI:0002451 ELISA measuring epitope specific interferon-alpha production by T cells
• OBI:0002452 biological activity assay measuring epitope specific interferon-alpha production by T cells
• OBI:0002453 health status inclusion criterion
• OBI:0002454 clinically relevant lifestyle inclusion criterion
• OBI:0002455 clinically relevant exposure inclusion criterion
• OBI:0002456 gravidity inclusion criterion

2017-11-07

This release includes 255 new terms since the 2017-09-03 release.

• OBI:0002189 local field potential recording
• OBI:0002190 courier organization
• OBI:0002191 courier tracking number
• OBI:0002192 Leica Peloris rapid tissue processor
• OBI:0002193 Thermo Fisher Scientific
• OBI:0002194 Microm Ergostar HM200
• OBI:0002195 microtome blade
• OBI:0002196 Sakura Low profile Accu-Edge microtome blade
• OBI:0002197 tissue section thickness
• OBI:0002198 molecular analysis facility organization
• OBI:0002199 reason for lack of data item
• OBI:0002200 cannot be assessed determination
• OBI:0002201 determination if assay will provide reliable results
• OBI:0002202 GX
• OBI:0002203 pTX
• OBI:0002204 pNX
• OBI:0002205 histologic grade according to AJCC 7th edition
• OBI:0002206 G1: Well differentiated
• OBI:0002207 G2: Moderately differentiated
• OBI:0002208 G3: Poorly differentiated
• OBI:0002209 G4: Undifferentiated
• OBI:0002210 histologic grade according to the Fuhrman Nuclear Grading System
• OBI:0002211 G1 (Fuhrman)
• OBI:0002212 G2 (Fuhrman)
• OBI:0002213 G3 (Fuhrman)
• OBI:0002214 G4 (Fuhrman)
• OBI:0002215 histologic grade for ovarian tumor
• OBI:0002216 histologic grade for ovarian tumor according to a two-tier grading system
• OBI:0002217 Low grade ovarian tumor
• OBI:0002218 High grade ovarian tumor
• OBI:0002219 histologic grade for ovarian tumor according to the World Health Organization
• OBI:0002220 G1 (WHO)
• OBI:0002221 G2 (WHO)
• OBI:0002222 G3 (WHO)
• OBI:0002223 G4 (WHO)
• OBI:0002224 pathologic primary tumor stage for colon and rectum according to AJCC 7th edition
• OBI:0002225 pT0 (colon)
• OBI:0002226 pTis (colon)
• OBI:0002227 pT1 (colon)
• OBI:0002228 pT2 (colon)
• OBI:0002229 pT3 (colon)
• OBI:0002230 pT4a (colon)
• OBI:0002231 pT4b (colon)
• OBI:0002232 pathologic primary tumor stage for lung according to AJCC 7th edition
• OBI:0002233 pT0 (lung)
• OBI:0002234 pTis (lung)
• OBI:0002235 pT1 (lung)
• OBI:0002236 pT1a (lung)
• OBI:0002237 pT1b (lung)
• OBI:0002238 pT2 (lung)
• OBI:0002239 pT2a (lung)
• OBI:0002240 pT2b (lung)
• OBI:0002241 pT3 (lung)
• OBI:0002242 pT4 (lung)
• OBI:0002243 pathologic primary tumor stage for kidney according to AJCC 7th edition
• OBI:0002244 pT0 (kidney)
• OBI:0002245 pT1 (kidney)
• OBI:0002246 pT1a (kidney)
• OBI:0002247 pT1b (kidney)
• OBI:0002248 pT2 (kidney)
• OBI:0002249 pT2a (kidney)
• OBI:0002250 pT2b (kidney)
• OBI:0002251 pT3 (kidney)
• OBI:0002252 pT3a (kidney)
• OBI:0002253 pT3b (kidney)
• OBI:0002254 pT3c (kidney)
• OBI:0002255 pT4 (kidney)
• OBI:0002256 pathologic primary tumor stage for ovary according to AJCC 7th edition
• OBI:0002257 pT0 (ovary)
• OBI:0002258 pT1 (ovary)
• OBI:0002259 pT1a (ovary)
• OBI:0002260 pT1b (ovary)
• OBI:0002261 pT1c (ovary)
• OBI:0002262 pT2 (ovary)
• OBI:0002263 pT2a (ovary)
• OBI:0002264 pT2b (ovary)
• OBI:0002265 pT2c (ovary)
• OBI:0002266 pT3 (ovary)
• OBI:0002267 pT3a (ovary)
• OBI:0002268 pT3b (ovary)
• OBI:0002269 pT3c (ovary)
• OBI:0002270 pathologic lymph node stage for colon and rectum according to AJCC 7th edition
• OBI:0002271 pN0 (colon)
• OBI:0002272 pN1 (colon)
• OBI:0002273 pN1a (colon)
• OBI:0002274 pN1b (colon)
• OBI:0002275 pN1c (colon)
• OBI:0002276 pN2 (colon)
• OBI:0002277 pN2a (colon)
• OBI:0002278 pN2b (colon)
• OBI:0002279 pathologic lymph node stage for lung according to AJCC 7th edition
• OBI:0002280 pN0 (lung)
• OBI:0002281 pN1 (lung)
• OBI:0002282 pN2 (lung)
• OBI:0002283 pN3 (lung)
• OBI:0002284 pathologic lymph node stage for kidney according to AJCC 7th edition
• OBI:0002285 pN0 (kidney)
• OBI:0002286 pN1 (kidney)
• OBI:0002287 pathologic lymph node stage for ovary according to AJCC 7th edition
• OBI:0002288 pN0 (ovary)
• OBI:0002289 pN1 (ovary)
• OBI:0002290 pathologic distant metastases stage for colon according to AJCC 7th edition
• OBI:0002291 cM0 (colon)
• OBI:0002292 cM1 (colon)
• OBI:0002293 cM1a (colon)
• OBI:0002294 cM1b (colon)
• OBI:0002295 pM1 (colon)
• OBI:0002296 pM1a (colon)
• OBI:0002297 pM1b (colon)
• OBI:0002298 pathologic distant metastases stage for lung according to AJCC 7th edition
• OBI:0002299 cM0 (lung)
• OBI:0002300 cM1 (lung)
• OBI:0002301 cM1a (lung)
• OBI:0002302 cM1b (lung)
• OBI:0002303 pM1 (lung)
• OBI:0002304 pM1a (lung)
• OBI:0002305 pM1b (lung)
• OBI:0002306 pathologic distant metastases stage for kidney according to AJCC 7th edition
• OBI:0002307 cM0 (kidney)
• OBI:0002308 cM1 (kidney)
• OBI:0002309 pM1 (kidney)
• OBI:0002310 pathologic distant metastases stage for ovary according to AJCC 7th edition
• OBI:0002311 cM0 (ovary)
• OBI:0002312 cM1 (ovary)
• OBI:0002313 pM1 (ovary)
• OBI:0002314 clinical tumor stage group according to AJCC 7th edition
• OBI:0002315 Occult Carcinoma (AJCC 7th)
• OBI:0002316 Stage 0 (AJCC 7th)
• OBI:0002317 Stage I (AJCC 7th)
• OBI:0002318 Stage IIA (AJCC 7th)
• OBI:0002319 Stage IIB (AJCC 7th)
• OBI:0002320 Stage IIC (AJCC 7th)
• OBI:0002321 Stage IIIA (AJCC 7th)
• OBI:0002322 Stage IIIB (AJCC 7th)
• OBI:0002323 Stage IIIC (AJCC 7th)
• OBI:0002324 Stage IVA (AJCC 7th)
• OBI:0002325 Stage IVB (AJCC 7th)
• OBI:0002326 International Federation of Gynecology and Obstetrics cervical cancer stage value specification
• OBI:0002327 Stage IA (FIGO)
• OBI:0002328 Stage IA1 (FIGO)
• OBI:0002329 Stage IA2 (FIGO)
• OBI:0002330 Stage IB (FIGO)
• OBI:0002331 Stage IB1 (FIGO)
• OBI:0002332 Stage IB2 (FIGO)
• OBI:0002333 Stage IIA (FIGO)
• OBI:0002334 Stage IIA1 (FIGO)
• OBI:0002335 Stage IIA2 (FIGO)
• OBI:0002336 Stage IIB (FIGO)
• OBI:0002337 Stage IIIA (FIGO)
• OBI:0002338 Stage IIIB (FIGO)
• OBI:0002339 Stage IVA (FIGO)
• OBI:0002340 Stage IVB (FIGO)
• OBI:0002341 International Federation of Gynecology and Obstetrics ovarian cancer stage value specification
• OBI:0002342 Stage 1 (FIGO)
• OBI:0002343 Stage 1A (FIGO)
• OBI:0002344 Stage 1B (FIGO)
• OBI:0002345 Stage 1C (FIGO)
• OBI:0002346 Stage 2 (FIGO)
• OBI:0002347 Stage 2A (FIGO)
• OBI:0002348 Stage 2B (FIGO)
• OBI:0002349 Stage 2C (FIGO)
• OBI:0002350 Stage 3 (FIGO)
• OBI:0002351 Stage 3A (FIGO)
• OBI:0002352 Stage 3B (FIGO)
• OBI:0002353 Stage 3C (FIGO)
• OBI:0002354 Stage 4 (FIGO)
• OBI:0002355 Stage Unknown (FIGO)
• OBI:0002356 performance status value specification
• OBI:0002357 Eastern Cooperative Oncology Group score value specification
• OBI:0002358 3: symptomatic in bed more than 50% of the day but not bed ridden
• OBI:0002359 2: symptomatic but in bed less than 50% of the day
• OBI:0002360 4: bed ridden
• OBI:0002361 0: asymptomatic
• OBI:0002362 1: symptomatic but fully ambulatory
• OBI:0002363 Karnofsky score vaue specification
• OBI:0002364 100: asymptomatic
• OBI:0002365 80-90: symptomatic but fully ambulatory
• OBI:0002366 60-70: symptomatic but in bed less than 50% of the day
• OBI:0002367 40-50: symptomatic, in bed more than 50% of the day, but not bed ridden
• OBI:0002368 clinical history of cancer
• OBI:0002369 clinical history devoid of cancer
• OBI:0002370 unknown clinical history of cancer
• OBI:0002371 diagnosis of cancer
• OBI:0002372 family clinical history of cancer
• OBI:0002373 aunt clinical history of cancer
• OBI:0002374 brother clinical history of cancer
• OBI:0002375 daughter clinical history of cancer
• OBI:0002376 father clinical history of cancer
• OBI:0002377 mother clinical history of cancer
• OBI:0002378 sister clinical history of cancer
• OBI:0002379 son clinical history of cancer
• OBI:0002380 uncle clinical history of cancer
• OBI:0002381 grandmother clinical history of cancer
• OBI:0002382 grandfather clinical history of cancer
• OBI:0002383 nephew clinical history of cancer
• OBI:0002384 niece clinical history of cancer
• OBI:0002385 diagnosis of infectious disease
• OBI:0002386 diagnosis of hepatitis B
• OBI:0002387 diagnosis of hepatitis C
• OBI:0002388 diagnosis of HIV
• OBI:0002389 clinical history of repeated HIV assays
• OBI:0002390 exposure to second hand smoke
• OBI:0002391 exposure to second hand smoke in household during childhood
• OBI:0002392 exposure to second hand smoke in current household
• OBI:0002393 pregnancy history
• OBI:0002394 number of pregnancies
• OBI:0002395 number of live births
• OBI:0002396 age when gave birth to first child
• OBI:0002397 gynecologic surgery history
• OBI:0002398 hysterectomy history
• OBI:0002399 unilateral oophorectomy history
• OBI:0002400 neither hysterectomy nor oophorectomy history
• OBI:0002401 hormonal birth control use history
• OBI:0002402 hormonal birth control former use history
• OBI:0002403 hormonal birth control current use history
• OBI:0002404 no hormonal birth control use history
• OBI:0002405 hormonal replacement therapy history
• OBI:0002406 delivery form for hormonal replacement therapy
• OBI:0002407 pill delivery form for hormonal replacement therapy
• OBI:0002408 patch delivery form for hormonal replacement therapy
• OBI:0002409 cream delivery form for hormonal replacement therapy
• OBI:0002410 menopausal status
• OBI:0002411 indeterminate menopausal status
• OBI:0002412 premenopausal status
• OBI:0002413 perimenopausal status
• OBI:0002414 postmenopausal status
• OBI:0002415 exposure to environmental and workplace carcinogens history
• OBI:0002416 exposure to arsenic history
• OBI:0002417 exposure to asbestos history
• OBI:0002418 exposure to diesel exhaust history
• OBI:0002419 exposure to chromium history
• OBI:0002420 exposure to silica history
• OBI:0002421 indicator of whether an inclusion criterion was met
• OBI:0002422 indicator of whether all inclusion criteria were met
• OBI:0002423 age of majority inclusion criterion
• OBI:0002424 chemotherapy treatment exclusion criterion
• OBI:0002425 radiation treatment exclusion criteria
• OBI:0002426 chemotherapy treatment within the recent past exclusion criterion
• OBI:0002427 r...

2017-09-03

This release includes 76 new terms since the 2017-02-22 release. It was built using a new ROBOT-based build system, which means there will be some slight differences in the generated files.

• OBI:0002133 cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells
• OBI:0002134 biological activity assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells
• OBI:0002135 has specified value
• OBI:0002136 RNA Integrity Number calculation
• OBI:0002137 RNA Integrity Number value specification
• OBI:0002138 temperature value specification
• OBI:0002139 volume value specification
• OBI:0002140 temperature measurement assay
• OBI:0002141 volume measurement assay
• OBI:0002142 Nanostring nCounter miRNA expression assay
• OBI:0002143 bromouride labeling and sequencing after UV exposure
• OBI:0002144 extrachromosomal circular DNA sequencing assay
• OBI:0002145 antigen specific antibodies assay
• OBI:0002146 HIV antibody assay
• OBI:0002147 HIV group O antibody assay
• OBI:0002148 surface HBV antibody assay
• OBI:0002149 core HBV antibody assay
• OBI:0002150 core HBV IgM antibody assay
• OBI:0002151 HCV antibody assay
• OBI:0002152 EBV IgG antibody assay
• OBI:0002153 EBV IgM antibody assay
• OBI:0002154 CMV antibody assay
• OBI:0002155 venereal disease research laboratory test
• OBI:0002156 rapid plasma reagin test
• OBI:0002157 HBV surface antigen assay
• OBI:0002158 HIV-1 nucleic acid testing
• OBI:0002159 HCV nucleic acid testing
• OBI:0002160 multiplexed indexed T7 ChIP-seq
• OBI:0002543 atrial appendage specimen
• OBI:0002544 esophagogastric junction specimen
• OBI:0002545 ileum specimen
• OBI:0002546 liver specimen
• OBI:0002547 minor salivary gland specimen
• OBI:0002548 omentum specimen
• OBI:0002549 ovary specimen
• OBI:0002550 sigmoid colon specimen
• OBI:0002551 suprapubic skin specimen
• OBI:0002552 testis specimen
• OBI:0002553 uterus specimen
• OBI:0002554 vagina specimen
• OBI:0002555 age group inclusion criterion
• OBI:0002556 minimum age value specification
• OBI:0002557 maximum age value specification
• OBI:0002558 use of medication inclusion criterion
• OBI:0002559 hospital patient inclusion criterion
• OBI:0002560 family status inclusion criterion
• OBI:0002561 sex inclusion criterion
• OBI:0002562 country of residence inclusion criteria
• OBI:0002563 ethnicity inclusion criterion
• OBI:0002564 histopathology
• OBI:0002161 systematic evolution of ligands by exponential enrichment assay
• OBI:0002162 footprinting assay
• OBI:0002163 DNAse footprinting assay
• OBI:0002164 mammalian 2-hybrid assay
• OBI:0002165 protein localization assay
• OBI:0002166 tissue-based protein localization assay
• OBI:0002167 subcellular protein localization assay
• OBI:0002168 subcellular protein immunohistochemistry assay
• OBI:0002169 ChIP-qPCR assay
• OBI:0002170 genomic SELEX
• OBI:0002171 dot blot assay
• OBI:0002172 Northwestern blot assay
• OBI:0002173 Southwestern blot assay
• OBI:0002174 immunocytochemistry
• OBI:0002175 ATP bioluminescence assay
• OBI:0002176 electrophysiology assay
• OBI:0002177 patch clamp assay
• OBI:0002178 whole-cell patch clamp assay
• OBI:0002179 cell-attached patch clamp assay
• OBI:0002180 inside-out patch clamp assay
• OBI:0002181 outside-out patch clamp assay
• OBI:0002182 voltage clamp assay
• OBI:0002183 two electrode voltage clamp assay
• OBI:0002184 cut open oocyte voltage clamp assay
• OBI:0002185 current clamp assay
• OBI:0002186 electroencephalography
• OBI:0002187 single-unit recording
• OBI:0002188 multi-unit recording
• OBI:0002189 local field potential recording

2017-02-22

There are 14 new classes since the 2016-10-11 release:

• OBI:0002123 IHC slide staining
• OBI:0002124 H&E slide staining
• OBI:0002125 H&E-stained fixed tissue slide specimen
• OBI:0002126 IHC-stained fixed tissue slide specimen
• OBI:0002127 single cell specimen
• OBI:0002128 Illumina Genome Analyzer
• OBI:0002129 Illumina HiSeq X Ten
• OBI:0002130 Illumina Infinium Omni5Exome-4 Kit
• OBI:0002131 Illumina Infinium MethylationEPIC BeadChip
• OBI:0002132 pulse stable isotope labeling by amino acids in cell culture
• CHMO:0000087 fluorescence microscopy
• CHMO:0000089 confocal fluorescence microscopy
• CHMO:0000102 light microscopy
• CHMO:0000701 liquid chromatography-tandem mass spectrometry

Four assay terms were adopted from the Chemical Methods Ontology, see: #777.

This is the first release to use our new GitHub repository. This release includes SVN commits r4084 through r4092 from the old repository. The commit history is on SourceForge http://sourceforge.net/p/obi/code/HEAD/log/ or on GitHub https://github.com/obi-ontology/obi-legacy-svn.