Merge branch 'master' into 1771_harmonize_solvent

README.md

@@ -1,6 +1,6 @@
 # Ontology for Biomedical Investigations
 
-[![Build Status](https://travis-ci.com/obi-ontology/obi.svg?branch=master)](https://travis-ci.com/obi-ontology/obi)
+[![GitHub Actions](https://github.com/obi-ontology/obi/actions/workflows/obi-test.yml/badge.svg)](https://github.com/obi-ontology/obi/actions/workflows/obi-test.yml)
 [![Powered by the ROBOT](https://img.shields.io/static/v1?label=Powered%20by&message=ROBOT&color=green&style=flat)](http://robot.obolibrary.org/)
 <a href="http://dashboard.obofoundry.org/dashboard/obi/dashboard.html"><img src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2Fobi%2Fdashboard-score-badge.json" /></a>
 <a href="http://dashboard.obofoundry.org/dashboard/obi/dashboard.html"><img src="https://img.shields.io/endpoint?url=https%3A%2F%2Fraw.githubusercontent.com%2FOBOFoundry%2Fobo-dash.github.io%2Fgh-pages%2Fdashboard%2Fobi%2Fdashboard-qc-badge.json" /></a>
@@ -151,7 +151,6 @@ We use git and GitHub to develop OBI. There's a lot of good documentation on bot
 
 - git [website](https://git-scm.com) with files and documentation
 - GitHub [Help](https://help.github.com) and [Flow](https://guides.github.com/introduction/flow/)
-- [git command-line overview](http://dont-be-afraid-to-commit.readthedocs.io/en/latest/git/commandlinegit.html)
 
 
 ## Initial Set Up

src/ontology/modules/study-designs.owl

@@ -2269,6 +2269,22 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0003658 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003658">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0500000"/>
+        <obo:IAO_0000111>ring trial design</obo:IAO_0000111>
+        <obo:IAO_0000112>https://eco-fab.org/about-ecofab-initiative/</obo:IAO_0000112>
+        <obo:IAO_0000115>A study design with the objective of establishing the reproducibility of an experimental approach by performing experiments in different laboratories under the same conditions and comparing the experimental outcomes.</obo:IAO_0000115>
+        <obo:IAO_0000117>Bjoern Peters</obo:IAO_0000117>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1768</obo:IAO_0000233>
+        <obo:IAO_0000234>Chris Mungall</obo:IAO_0000234>
+        <rdfs:label>ring trial design</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0100026"/>

src/ontology/obi-edit.owl

@@ -22033,6 +22033,25 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0003656 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003656">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0302885"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_15377"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <obo:IAO_0000111 xml:lang="en">water filtration</obo:IAO_0000111>
+        <obo:IAO_0000115 xml:lang="en">A filtration process of water intended to remove or reduce the concentration of particulate matter, such as suspended particles, parasites, bacteria, algae, viruses, and fungi, as well as other undesirable chemical and biological contaminants.</obo:IAO_0000115>
+        <obo:IAO_0000117>Anoosha Sehar https://orcid.org/0000-0001-5275-8866</obo:IAO_0000117>
+        <obo:IAO_0000234>GENEPIO</obo:IAO_0000234>
+        <rdfs:label xml:lang="en">water filtration</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0003657 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003657">

src/ontology/templates/study-designs.tsv

@@ -77,6 +77,7 @@ OBI:0002624	case-control study design				A study design that entails the creatio
 OBI:0002674	case series design	case series study design	ready for release		A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included.	https://www.ncbi.nlm.nih.gov/pubmed/22213493	PMID: 22213493	http://orcid.org/0000-0002-8844-9165					subclass	study design						
 OBI:0002945	population based design	population based design			A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment.	https://link.springer.com/referenceworkentry/10.1007%2F978-1-4419-1005-9_45, EFO_0001430 population based design		Chris Stoeckert				https://github.com/obi-ontology/obi/issues/1090	subclass	study design						
 OBI:0003291	in silico design				A study design that is executed primarily on a computer.	https://en.wikipedia.org/wiki/In_silico		Hector Guzman-Orozco			CMI-PB	https://github.com/obi-ontology/obi/issues/1430	subclass	study design						
+OBI:0003658	ring trial design	ring trial design			A study design with the objective of establishing the reproducibility of an experimental approach by performing experiments in different laboratories under the same conditions and comparing the experimental outcomes.		https://eco-fab.org/about-ecofab-initiative/	Bjoern Peters|Sebastian Duesing			Chris Mungall	https://github.com/obi-ontology/obi/issues/1768	subclass	study design						
 OBI:0300310	sequential design	sequential design	pending final vetting		Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits.  Enrollment is continued if the difference does not exceed the limits.  It is terminated if it does	MUSC	PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.	Philippe Rocca-Serra		Provenance: OCI			subclass	intervention design						
 OBI:0300311	observation design	observation design	pending final vetting		observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.	OBI branch derived	PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.	Philippe Rocca-Serra					subclass	study design						
 OBI:0500001	clinical study design	clinical study design	pending final vetting		Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]	Clinical Research Glossary Version 4.0 CDICS glossary group	PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.	PlanAndPlannedProcess Branch	The definition needs to be extended to other things than simply patients				subclass	study design