nicolevasilevsky
commented
2 years ago @cthoyt Mondo did have an active publication (but I added another one with #1849). But maybe you want to check your code to generate the table?
Closed cthoyt closed 1 year ago
nicolevasilevsky
commented
2 years ago @cthoyt Mondo did have an active publication (but I added another one with #1849). But maybe you want to check your code to generate the table?
cthoyt
commented
2 years ago @cthoyt Mondo did have an active publication (but I added another one with #1849). But maybe you want to check your code to generate the table?
There's a difference between the publications entry within a usages entry, which corresponds to publications about the usage itself, and the top-level publications field, which refers to publications about the ontology itself. Mondo is indeed missing the top-level publications field, so I think the code is fine, but thanks for double checking. I'll make a comment on #1849 for posterity as well.
matentzn
commented
2 years ago There was an interesting debate on publications here as well: https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1846 just not to lose it when the archeologists come to this issue.
nicolevasilevsky
commented
2 years ago @cthoyt my bad, it was me, not you. :) Thanks for clarifying.
gkoutos
commented
2 years ago Hi Charles,
Many thanks for your email and for pointing this out.
Could you please add the following papers to cite for
NBO: PMID: 24177753
And for
PATO: PMID: 28387809 and PMID: 15642100
Many thanks !
George
On 9 Apr 2022, at 18:35, Charles Tapley Hoyt @.***> wrote:
Currently, 151 ontologies in the OBO Foundry do not have a publications: entry in their metadata. This field is used to generate the citation information on the ontology page (see image below with ChEBI as an example)
Inside the metadata, this looks like the following, with an id: field containing a URL based on a PubMed identifier and a title: that can be free text. The publications: field is a list and it's also possible to have multiple entries, each with their own id and title. Here's what the metadata looks like for ChEBI:
Ontologies Missing Publications
The following is table with all of the ontologies that are missing the publications field including a tag for the responsible person for each. You can use the following template in your ontology's metadata by replacing
and with your ontology's publication information:</p> <p>publications : </p> <ul> <li> <p>id: <a href="https://www.ncbi.nlm.nih.gov/pubmed/">https://www.ncbi.nlm.nih.gov/pubmed/</a><PUBMED></p> </li> </ul> <p>title: "<TITLE>" There's an "edit" button for each row of the table which will bring you directly to the place where you can edit your ontology's metadata in browser.</p> <p>Prefix Title Contact Edit bfo Basic Formal Ontology @phismith edit go Gene Ontology @suzialeksander edit obi Ontology for Biomedical Investigations @bpeters42 edit pato Phenotype And Trait Ontology @gkoutos edit aism Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) @JCGiron edit amphx The Amphioxus Development and Anatomy Ontology @hescriva edit apo Ascomycete phenotype ontology @srengel edit apollo_sv Apollo Structured Vocabulary @mbrochhausen edit aro Antibiotic Resistance Ontology @agmcarthur edit bco Biological Collections Ontology @ramonawalls edit caro Common Anatomy Reference Ontology @mellybelly edit cdao Comparative Data Analysis Ontology @balhoff edit cdno Compositional Dietary Nutrition Ontology @LilyAndres edit cheminf Chemical Information Ontology @egonw edit chiro CHEBI Integrated Role Ontology @nicolevasilevsky edit chmo Chemical Methods Ontology @batchelorc edit cido Coronavirus Infectious Disease Ontology @yongqunh edit cio Confidence Information Ontology @fbastian edit clao Collembola Anatomy Ontology @luis-gonzalez-m edit clo Cell Line Ontology @siiraa edit clyh Clytia hemisphaerica Development and Anatomy Ontology @L-Leclere edit cob Core Ontology for Biology and Biomedicine @bpeters42 edit colao Coleoptera Anatomy Ontology (COLAO) @JCGiron edit cro Contributor Role Ontology @marijane edit cteno Ctenophore Ontology @cmungall edit cto CTO: Core Ontology of Clinical Trials @akodamullil edit cvdo Cardiovascular Disease Ontology @pfabry edit ddanat Dictyostelium discoideum anatomy @pfey03 edit ddpheno Dictyostelium discoideum phenotype ontology @pfey03 edit dideo Drug-drug Interaction and Drug-drug Interaction Evidence Ontology @mbrochhausen edit disdriv Disease Drivers Ontology @lschriml edit dron The Drug Ontology @hoganwr edit duo Data Use Ontology @mcourtot edit ecao The Echinoderm Anatomy and Development Ontology @ettensohn edit ecocore An ontology of core ecological entities @pbuttigieg edit ecto Environmental conditions, treatments and exposures ontology @diatomsRcool edit emapa Mouse Developmental Anatomy Ontology @tfhayamizu edit epio Epilepsy Ontology @akodamullil edit eupath VEuPathDB ontology @cstoeckert edit exo Exposure ontology @diatomsRcool edit fao Fungal gross anatomy @ValWood edit fbbi Biological Imaging Methods Ontology @wawong edit fbcv FlyBase Controlled Vocabulary @Clare72 edit fbdv Drosophila development @Clare72 edit fideo Food Interactions with Drugs Evidence Ontology @getbordea edit flopo Flora Phenotype Ontology @leechuck edit fobi Food-Biomarker Ontology @pcastellanoescuder edit foodon Food Ontology @ddooley edit fovt FuTRES Ontology of Vertebrate Traits @megbalk edit gecko Genomics Cohorts Knowledge Ontology @beckyjackson edit genepio Genomic Epidemiology Ontology @ddooley edit geno Genotype Ontology @mbrush edit geo Geographical Entity Ontology @hoganwr edit gno Glycan Naming and Subsumption Ontology (GNOme) @edwardsnj edit hancestro Human Ancestry Ontology @daniwelter edit hao Hymenoptera Anatomy Ontology @mjy edit hom Homology Ontology @fbastian edit hsapdv Human Developmental Stages @fbastian edit hso Health Surveillance Ontology @nandadorea edit htn Hypertension Ontology @aellenhicks edit iao Information Artifact Ontology @zhengj2007 edit iceo Integrative and Conjugative Element Ontology @Lemon-Liu edit ico Informed Consent Ontology @yongqunh edit ido Infectious Disease Ontology @lgcowell edit ino Interaction Network Ontology @yongqunh edit labo clinical LABoratory Ontology @pfabry edit lepao Lepidoptera Anatomy Ontology @luis-gonzalez-m edit ma Mouse adult gross anatomy @tfhayamizu edit maxo Medical Action Ontology @LCCarmody edit mco Microbial Conditions Ontology @citmejia edit mf Mental Functioning Ontology @jannahastings edit mfmo Mammalian Feeding Muscle Ontology @RDruzinsky edit mfoem Emotion Ontology @jannahastings edit mfomd Mental Disease Ontology @jannahastings edit mi Molecular Interactions Controlled Vocabulary @pporrasebi edit miapa MIAPA Ontology @hlapp edit micro Ontology of Prokaryotic Phenotypic and Metabolic Characters @carrineblank edit mmusdv Mouse Developmental Stages @fbastian edit mondo Mondo Disease Ontology @nicolevasilevsky edit mop Molecular Process Ontology @batchelorc edit mp Mammalian Phenotype Ontology @sbello edit mpath Mouse pathology ontology @PaulNSchofield edit mpio Minimum PDDI Information Ontology @mbrochhausen edit mro MHC Restriction Ontology @bpeters42 edit nbo Neuro Behavior Ontology @gkoutos edit ncbitaxon NCBI organismal classification @fbastian edit ncit NCI Thesaurus OBO Edition @mellybelly edit ncro Non-Coding RNA Ontology @Huang-OMIT edit nomen NOMEN - A nomenclatural ontology for biological names @mjy edit oae Ontology of Adverse Events @yongqunh edit oarcs Ontology of Arthropod Circulatory Systems @mjy edit oba Ontology of Biological Attributes @cmungall edit obcs Ontology of Biological and Clinical Statistics @zhengj2007 edit obib Ontology for Biobanking @zhengj2007 edit ogg The Ontology of Genes and Genomes @yongqunh edit ogms Ontology for General Medical Science @BAevermann edit ogsf Ontology of Genetic Susceptibility Factor @linikujp edit ohd Oral Health and Disease Ontology @wdduncan edit ohmi Ontology of Host-Microbiome Interactions @yongqunh edit ohpi Ontology of Host Pathogen Interactions @e4ong1031 edit olatdv Medaka Developmental Stages @fbastian edit omit Ontology for MIRNA Target @Huang-OMIT edit omo OBO Metadata Ontology @cmungall edit omp Ontology of Microbial Phenotypes @jimhu-tamu edit omrse Ontology of Medically Related Social Entities @hoganwr edit one Ontology for Nutritional Epidemiology @cyang0128 edit ons Ontology for Nutritional Studies @FrancescoVit edit ontoavida OntoAvida: ontology for Avida digital evolution platform @miguelfortuna edit ontoneo Obstetric and Neonatal Ontology @FernandaFarinelli edit oostt Ontology of Organizational Structures of Trauma centers and Trauma systems @mbrochhausen edit opl Ontology for Parasite LifeCycle @zhengj2007 edit opmi Ontology of Precision Medicine and Investigation @yongqunh edit ornaseq Ontology of RNA Sequencing @safisher edit ovae Ontology of Vaccine Adverse Events @yongqunh edit pcl Provisional Cell Ontology @dosumis edit pco Population and Community Ontology @ramonawalls edit pdro The Prescription of Drugs Ontology @pfabry edit pdumdv Platynereis Developmental Stages @fbastian edit phipo Pathogen Host Interaction Phenotype Ontology @CuzickA edit plana planaria-ontology @srobb1 edit planp Planarian Phenotype Ontology @srobb1 edit ppo Plant Phenology Ontology @ramonawalls edit psdo Performance Summary Display Ontology @zachll edit pso Plant Stress Ontology @cooperl09 edit rbo Radiation Biology Ontology @DanBerrios edit ro Relation Ontology @cmungall edit rxno Name Reaction Ontology @batchelorc edit sepio Scientific Evidence and Provenance Information Ontology @mbrush edit spd Spider Ontology @martinjramirez edit stato The Statistical Methods Ontology @agbeltran edit swo Software ontology @allysonlister edit symp Symptom Ontology @lschriml edit taxrank Taxonomic rank vocabulary @balhoff edit trans Pathogen Transmission Ontology @lschriml edit tto Teleost taxonomy ontology @balhoff edit txpo Toxic Process Ontology @yuki-yamagata edit uo Units of measurement ontology @gkoutos edit upheno Unified phenotype ontology (uPheno) @nicolevasilevsky edit vo Vaccine Ontology @yongqunh edit vt Vertebrate trait ontology @caripark edit vto Vertebrate Taxonomy Ontology @balhoff edit xlmod HUPO-PSI cross-linking and derivatization reagents controlled vocabulary @lutzfischer edit xpo Xenopus Phenotype Ontology @seger edit zeco Zebrafish Experimental Conditions Ontology @ybradford edit zfs Zebrafish developmental stages ontology @cerivs edit zp Zebrafish Phenotype Ontology @ybradford edit gsso Gender, Sex, and Sexual Orientation (GSSO) ontology @Superraptor edit kisao Kinetic Simulation Algorithm Ontology @jonrkarr edit mamo Mathematical modeling ontology @gambardella edit sbo Systems Biology Ontology @rsmsheriff edit scdo Sickle Cell Disease Ontology @JadeHotchkiss edit Code</p> <p>The code that was used to generate this table — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.</p> </blockquote> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/pfey03"><img src="https://avatars.githubusercontent.com/u/1349602?v=4" />pfey03</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Hello Charles, For Dicty ontologies please use these papers</p> <p>DDANAT use PMID: 18366659 DDPHENO use PMID: 31840793</p> <p>Many thanks, Petra</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Ping to the following responsible contacts, who might not have got a notification because of the apparent 45-tag maximum in an issue: </p> <p>@BAevermann, @Clare72, @CuzickA, @DanBerrios, @FernandaFarinelli, @FrancescoVit, @Huang-OMIT, @JCGiron, @JadeHotchkiss, @L-Leclere, @LCCarmody, @Lemon-Liu, @LilyAndres, @PaulNSchofield, @RDruzinsky, @Superraptor, @ValWood, @aellenhicks, @agbeltran, @akodamullil, @allysonlister, @balhoff, @batchelorc, @beckyjackson, @bpeters42, @caripark, @carrineblank, @cerivs, @citmejia, @cmungall, @cooperl09, @cstoeckert, @cyang0128, @daniwelter, @ddooley, @diatomsRcool, @dosumis, @e4ong1031, @edwardsnj, @ettensohn, @fbastian, @getbordea, @hescriva, @hlapp</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Ping (part 2) to the following responsible contacts, who might not have got a notification because of the apparent 45-tag maximum in an issue:</p> <p>@hoganwr, @jannahastings, @jimhu-tamu, @jonrkarr, @leechuck, @lgcowell, @linikujp, @lschriml, @luis-gonzalez-m, @lutzfischer, @marijane, @martinjramirez, @mbrochhausen, @mbrush, @mcourtot, @megbalk, @mellybelly, @miguelfortuna, @mjy, @nandadorea, @pbuttigieg, @pfabry, @phismith, @pporrasebi, @ramonawalls, @rsmsheriff, @safisher, @sbello, @srengel, @srobb1, @suzialeksander, @tfhayamizu, @wawong, @wdduncan, @ybradford, @yongqunh, @yuki-yamagata, @zachll, @zhengj2007</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/LCCarmody"><img src="https://avatars.githubusercontent.com/u/26067008?v=4" />LCCarmody</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>There isn't a primary article foR MAxO (it is in preparation). Only papers referring to collaborations. Do you want these, too?</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/ettensohn"><img src="https://avatars.githubusercontent.com/u/64486247?v=4" />ettensohn</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Please remove me from this email chain!!!!</p> <p>On Thu, May 5, 2022 at 3:55 AM Charles Tapley Hoyt <strong><em>@</em></strong>.***> wrote:</p> <blockquote> <p>Ping (part 2) to the following responsible contacts, who might not have got a notification because of the apparent 45-tag maximum in an issue:</p> <p>@hoganwr <a href="https://github.com/hoganwr">https://github.com/hoganwr</a>, @jannahastings <a href="https://github.com/jannahastings">https://github.com/jannahastings</a>, @jimhu-tamu <a href="https://github.com/jimhu-tamu">https://github.com/jimhu-tamu</a>, @jonrkarr <a href="https://github.com/jonrkarr">https://github.com/jonrkarr</a>, @leechuck <a href="https://github.com/leechuck">https://github.com/leechuck</a>, @lgcowell <a href="https://github.com/lgcowell">https://github.com/lgcowell</a>, @linikujp <a href="https://github.com/linikujp">https://github.com/linikujp</a>, @lschriml <a href="https://github.com/lschriml">https://github.com/lschriml</a>, @luis-gonzalez-m <a href="https://github.com/luis-gonzalez-m">https://github.com/luis-gonzalez-m</a>, @lutzfischer <a href="https://github.com/lutzfischer">https://github.com/lutzfischer</a>, @marijane <a href="https://github.com/marijane">https://github.com/marijane</a>, @martinjramirez <a href="https://github.com/martinjramirez">https://github.com/martinjramirez</a>, @mbrochhausen <a href="https://github.com/mbrochhausen">https://github.com/mbrochhausen</a>, @mbrush <a href="https://github.com/mbrush">https://github.com/mbrush</a>, @mcourtot <a href="https://github.com/mcourtot">https://github.com/mcourtot</a>, @megbalk <a href="https://github.com/megbalk">https://github.com/megbalk</a>, @mellybelly <a href="https://github.com/mellybelly">https://github.com/mellybelly</a>, @miguelfortuna <a href="https://github.com/miguelfortuna">https://github.com/miguelfortuna</a>, @mjy <a href="https://github.com/mjy">https://github.com/mjy</a>, @nandadorea <a href="https://github.com/nandadorea">https://github.com/nandadorea</a>, @pbuttigieg <a href="https://github.com/pbuttigieg">https://github.com/pbuttigieg</a>, @pfabry <a href="https://github.com/pfabry">https://github.com/pfabry</a>, @phismith <a href="https://github.com/phismith">https://github.com/phismith</a>, @pporrasebi <a href="https://github.com/pporrasebi">https://github.com/pporrasebi</a>, @ramonawalls <a href="https://github.com/ramonawalls">https://github.com/ramonawalls</a>, @rsmsheriff <a href="https://github.com/rsmsheriff">https://github.com/rsmsheriff</a>, @safisher <a href="https://github.com/safisher">https://github.com/safisher</a>, @sbello <a href="https://github.com/sbello">https://github.com/sbello</a>, @srengel <a href="https://github.com/srengel">https://github.com/srengel</a>, @srobb1 <a href="https://github.com/srobb1">https://github.com/srobb1</a>, @suzialeksander <a href="https://github.com/suzialeksander">https://github.com/suzialeksander</a>, @tfhayamizu <a href="https://github.com/tfhayamizu">https://github.com/tfhayamizu</a>, @wawong <a href="https://github.com/wawong">https://github.com/wawong</a>, @wdduncan <a href="https://github.com/wdduncan">https://github.com/wdduncan</a>, @ybradford <a href="https://github.com/ybradford">https://github.com/ybradford</a>, @yongqunh <a href="https://github.com/yongqunh">https://github.com/yongqunh</a>, @yuki-yamagata <a href="https://github.com/yuki-yamagata">https://github.com/yuki-yamagata</a>, @zachll <a href="https://github.com/zachll">https://github.com/zachll</a>, @zhengj2007 <a href="https://github.com/zhengj2007">https://github.com/zhengj2007</a></p> <p>— Reply to this email directly, view it on GitHub <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118269687">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118269687</a>, or unsubscribe <a href="https://github.com/notifications/unsubscribe-auth/APL7WZ3NKCXMZKAIGJCXPTDVIN5HTANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/APL7WZ3NKCXMZKAIGJCXPTDVIN5HTANCNFSM5S7REGLA</a> . You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></p> </blockquote> <p>-- Dr. Charles A. Ettensohn Professor of Biological Sciences Carnegie Mellon University Tel: 412-268-5849 Email: <strong><em>@</em></strong>.***</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>@ettensohn you're listed as the contact person for ECAO <a href="https://obofoundry.org/ontology/ecao">https://obofoundry.org/ontology/ecao</a>, which is currently missing a publication annotation in the OBO Foundry. Is this not you? Or do you no longer wish to be listed as the responsible person for this ontology? If that's the case, can you either suggest an alternative contact person, or that we should mark it as "orphaned"?</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/tfhayamizu"><img src="https://avatars.githubusercontent.com/u/913577?v=4" />tfhayamizu</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Don't know why I received this email. Appears I was cc'd. I have no association with the echinoderm anatomy ontology.</p> <p>Terry</p> <p>On 5/5/22, 9:51 AM, Charles Tapley Hoyt <strong><em>@</em></strong>.<strong>**</strong>@<strong><em>.</em></strong>>> wrote:</p> <p>@ettensohn<a href="https://github.com/ettensohn">https://github.com/ettensohn</a> you're listed as the contact person for ECAO <a href="https://obofoundry.org/ontology/ecao">https://obofoundry.org/ontology/ecao</a>, which is currently missing a publication annotation in the OBO Foundry. Is this not you? Or do you no longer wish to be listed as the responsible person for this ontology?</p> <h2>— Reply to this email directly, view it on GitHub<a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118580912">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118580912</a>, or unsubscribe<a href="https://github.com/notifications/unsubscribe-auth/AAG7BKJCHMMIL7WTXKFDSETVIPG6VANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/AAG7BKJCHMMIL7WTXKFDSETVIPG6VANCNFSM5S7REGLA</a>. You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></h2> <p>The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/lschriml"><img src="https://avatars.githubusercontent.com/u/4333069?v=4" />lschriml</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Thank you @cthoyt - the Human Disease Ontology already has two publications included. Cheers, Lynn</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>@tfhayamizu you're listed as the contact for <a href="http://www.obofoundry.org/ontology/ma">MA</a> and <a href="http://www.obofoundry.org/ontology/emapa">EMAPA</a>, which both don't have publications. Are you not the right contact for those? or no longer want to be listed as the contact and have an alternative contact?</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>@lschriml you're also listed as responsible for <code>disdriv</code>, <code>trans</code>, and <code>symp</code></p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/batchelorc"><img src="https://avatars.githubusercontent.com/u/1147957?v=4" />batchelorc</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>No publications as yet, sorry.</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/JadeHotchkiss"><img src="https://avatars.githubusercontent.com/u/25898078?v=4" />JadeHotchkiss</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Updated SCDO #1894 </p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/hlapp"><img src="https://avatars.githubusercontent.com/u/51458?v=4" />hlapp</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>No publications. (And @cthoyt please remove me being tagged, assuming the purpose of tagging was a <em>ping</em>, not a forced CC on every future comment on this ticket?)</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/cthoyt"><img src="https://avatars.githubusercontent.com/u/5069736?v=4" />cthoyt</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>For anyone who has responded and doesn't want to keep getting notifications, there's an unsubscribe button at the top of the page (or check the tutorial on how to use the notification center on GitHub like a power user - <a href="https://docs.github.com/en/account-and-profile/managing-subscriptions-and-notifications-on-github/managing-subscriptions-for-activity-on-github/managing-your-subscriptions">https://docs.github.com/en/account-and-profile/managing-subscriptions-and-notifications-on-github/managing-subscriptions-for-activity-on-github/managing-your-subscriptions</a>)</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/tfhayamizu"><img src="https://avatars.githubusercontent.com/u/913577?v=4" />tfhayamizu</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>For the MA: Hayamizu TF, Mangan M, Corradi JP, Kadin JA, Ringwald M (2005). The Adult Mouse Anatomical Dictionary: A tool for annotating and integrating data. Genome Biology 6:R29.</p> <p>For the EMAPA:</p> <ol> <li>Bard JBL, Kaufman MH, Dubreuil C, Brune RM, Burger A, Baldock RA, Davidson DR (1998). An internet-accessible database of mouse developmental anatomy based on a systematic nomenclature. Mech Dev 74, 111-120.</li> <li>Hayamizu TF, Wicks MN, Davidson DR, Burger A, Ringwald M, Baldock RA (2013). EMAP/EMAPA ontology of mouse developmental anatomy: 2013 update. Journal of Biomedical Semantics 4:15.</li> <li>Hayamizu TF, Baldock RA, Ringwald M (2015). Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data. Mamm Genome 26, 422-30.</li> </ol> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/lschriml"><img src="https://avatars.githubusercontent.com/u/4333069?v=4" />lschriml</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>@cthoyt - yes I am the PI for : disdriv, trans, and symp</p> <ul> <li>I have not added a publication to their ontologies yet </li> </ul> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/LilyAndres"><img src="https://avatars.githubusercontent.com/u/25215773?v=4" />LilyAndres</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Hello,</p> <p>I thought I updated the md file when you first sent the notification but I can't see the changes, I tried to do the pull request but maybe I'm missing something... For CDNO please add the following:</p> <p>homepage: <a href="https://cdno.info/">https://cdno.info/</a> publications:</p> <ul> <li>id: <a href="https://doi.org/10.1002/csc2.20092">https://doi.org/10.1002/csc2.20092</a> title: "<Knowledge representation and data sharing to unlock crop variation for nutritional food security>"</li> </ul> <p>Please let me know if you have any issues with it.</p> <p>Regards,</p> <p>Lili</p> <p>Liliana Andres Hernandez, PhD</p> <p>Southern Cross Plant Science | Southern Cross University | PO Box 157 | LISMORE NSW 2480, AUSTRALIA</p> <p>[scps_new_std] [cid:282cca04-9b87-4cf0-8b32-f9fba8139b88]</p> <p>E: <strong><em>@</em></strong>.*** W: <a href="https://github.com/LilyAndres">https://github.com/LilyAndres</a></p> <p>I acknowledge the Bundjalung people as traditional owners and custodians of the land on which I work and live.</p> <hr /> <p>From: lschriml <strong><em>@</em></strong>.<strong><em>> Sent: Friday, 6 May 2022 3:38 AM To: OBOFoundry/OBOFoundry.github.io </em></strong>@<strong><em>.</em></strong>> Cc: Liliana Andres Hernandez <strong><em>@</em></strong>.<strong><em>>; Mention </em></strong>@<strong><em>.</em></strong>> Subject: Re: [OBOFoundry/OBOFoundry.github.io] Call to add publications to ontology metadata (Issue #1826)</p> <p>@cthoyt<a href="https://github.com/cthoyt">https://github.com/cthoyt</a> - yes I am the PI for : disdriv, trans, and symp</p> <ul> <li>I have not added a publication to their ontologies yet</li> </ul> <p>— Reply to this email directly, view it on GitHub<a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187</a>, or unsubscribe<a href="https://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA</a>. You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/yuki-yamagata"><img src="https://avatars.githubusercontent.com/u/54423214?v=4" />yuki-yamagata</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Hi @cthoyt </p> <p>Could you add the paper?</p> <p>TXPO: PMID:32883995 PMCID:PMC7471325 DOI: 10.1038/s41598-020-71370-7 Title: Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management</p> <p>I appreciate your support!</p> <p>Yuki</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/Clare72"><img src="https://avatars.githubusercontent.com/u/38460997?v=4" />Clare72</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>No pubs for FBdv and FBcv (there is one for dpo, which is incorporated into FBcv, but this is already linked to dpo).</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/martinjramirez"><img src="https://avatars.githubusercontent.com/u/24918048?v=4" />martinjramirez</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Hello,</p> <p>I am not sure of this email chain, but we have this publication for SPD:</p> <p>Ramírez, M. J., & Michalik, P. (2019). The spider anatomy ontology (SPD)a versatile tool to link anatomy with cross-disciplinary data. Diversity, 11(10), 202. <a href="https://doi.org/10.3390/d11100202">https://doi.org/10.3390/d11100202</a></p> <p>Best wishes,</p> <p>Martin Ramirez</p> <p>At 21:55 5/5/2022, Liliana Andres wrote:</p> <blockquote> <p>Hello,</p> <p>I thought I updated the md file when you first sent the notification but I can't see the changes, I tried to do the pull request but maybe I'm missing something... For CDNO please add the following:</p> <p>homepage: <a href="https://cdno.info/">https://cdno.info/</a> publications:</p> <ul> <li>id: <a href="https://doi.org/10.1002/csc2.20092">https://doi.org/10.1002/csc2.20092</a> title: "<Knowledge representation and data sharing to unlock crop variation for nutritional food security>"</li> </ul> <p>Please let me know if you have any issues with it.</p> <p>Regards,</p> <p>Lili</p> <p>Liliana Andres Hernandez, PhD</p> <p>Southern Cross Plant Science | Southern Cross University | PO Box 157 | LISMORE NSW 2480, AUSTRALIA</p> <p>[scps_new_std] [cid:282cca04-9b87-4cf0-8b32-f9fba8139b88]</p> <p>E: <strong><em>@</em></strong>.*** W: <a href="https://github.com/LilyAndres">https://github.com/LilyAndres</a></p> <p>I acknowledge the Bundjalung people as traditional owners and custodians of the land on which I work and live.</p> <hr /> <p>From: lschriml <strong><em>@</em></strong>.<strong><em>> Sent: Friday, 6 May 2022 3:38 AM To: OBOFoundry/OBOFoundry.github.io </em></strong>@<strong><em>.</em></strong>> Cc: Liliana Andres Hernandez <strong><em>@</em></strong>.<strong><em>>; Mention </em></strong>@<strong><em>.</em></strong>> Subject: Re: [OBOFoundry/OBOFoundry.github.io] Call to add publications to ontology metadata (Issue #1826)</p> <p><strong><em>@</em></strong>.***<a href="https://github.com/cthoyt">https://github.com/cthoyt</a> - yes I am the PI for : disdriv, trans, and symp</p> <ul> <li>I have not added a publication to their ontologies yet</li> </ul> <p> Reply to this email directly, view it on GitHub<a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187</a>, or unsubscribe<a href="https://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA</a>. You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></p> <p> Reply to this email directly, <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1119171442">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1119171442</a>view it on GitHub, or <a href="https://github.com/notifications/unsubscribe-auth/AF6DQIBJXCNSRAEOHAVC6ATVIRUZ3ANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/AF6DQIBJXCNSRAEOHAVC6ATVIRUZ3ANCNFSM5S7REGLA</a>unsubscribe. You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></p> </blockquote> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/suzialeksander"><img src="https://avatars.githubusercontent.com/u/13735608?v=4" />suzialeksander</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>@cthoyt can you add the following two publications for GO:</p> <p>Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. May 2000;25(1):25-9. [<a href="https://www.ncbi.nlm.nih.gov/pubmed/10802651">abstract</a> | <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/">full text</a>] The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. Jan 2021;49(D1):D325-D334. [<a href="https://pubmed.ncbi.nlm.nih.gov/33290552/">abstract</a> | <a href="https://academic.oup.com/nar/article-pdf/49/D1/D325/35364517/gkaa1113.pdf">full text</a>]</p> <p>thanks</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/srengel"><img src="https://avatars.githubusercontent.com/u/13241825?v=4" />srengel</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>reference for the APO: Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database; doi: 10.1093/database/bap001. [PMID: 20157474]</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/CuzickA"><img src="https://avatars.githubusercontent.com/u/11753634?v=4" />CuzickA</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Hi @cthoyt, PHIPO (The Pathogen Host Interaction Phenotype Ontology) does not have its own publication yet but is briefly described in PMID: 34788826. Please could you add this reference for now. Thanks, Alayne</p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/wdduncan"><img src="https://avatars.githubusercontent.com/u/3186638?v=4" />wdduncan</a> commented <strong> 2 years ago</strong> </div> <div class="markdown-body"> <p>Added citation for the OHD.<br /> <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/pull/2102">https://github.com/OBOFoundry/OBOFoundry.github.io/pull/2102</a> </p> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/hoganwr"><img src="https://avatars.githubusercontent.com/u/1253110?v=4" />hoganwr</a> commented <strong> 1 year ago</strong> </div> <div class="markdown-body"> <p>I've added pubs to as many ontologies as I can. GEO doesn't have a publication that meets the requirements (DOI, PubMed, or similar).</p> <p>On Thu, May 5, 2022 at 3:55 AM Charles Tapley Hoyt <strong><em>@</em></strong>.***> wrote:</p> <blockquote> <p>Ping (part 2) to the following responsible contacts, who might not have got a notification because of the apparent 45-tag maximum in an issue:</p> <p>@hoganwr <a href="https://github.com/hoganwr">https://github.com/hoganwr</a>, @jannahastings <a href="https://github.com/jannahastings">https://github.com/jannahastings</a>, @jimhu-tamu <a href="https://github.com/jimhu-tamu">https://github.com/jimhu-tamu</a>, @jonrkarr <a href="https://github.com/jonrkarr">https://github.com/jonrkarr</a>, @leechuck <a href="https://github.com/leechuck">https://github.com/leechuck</a>, @lgcowell <a href="https://github.com/lgcowell">https://github.com/lgcowell</a>, @linikujp <a href="https://github.com/linikujp">https://github.com/linikujp</a>, @lschriml <a href="https://github.com/lschriml">https://github.com/lschriml</a>, @luis-gonzalez-m <a href="https://github.com/luis-gonzalez-m">https://github.com/luis-gonzalez-m</a>, @lutzfischer <a href="https://github.com/lutzfischer">https://github.com/lutzfischer</a>, @marijane <a href="https://github.com/marijane">https://github.com/marijane</a>, @martinjramirez <a href="https://github.com/martinjramirez">https://github.com/martinjramirez</a>, @mbrochhausen <a href="https://github.com/mbrochhausen">https://github.com/mbrochhausen</a>, @mbrush <a href="https://github.com/mbrush">https://github.com/mbrush</a>, @mcourtot <a href="https://github.com/mcourtot">https://github.com/mcourtot</a>, @megbalk <a href="https://github.com/megbalk">https://github.com/megbalk</a>, @mellybelly <a href="https://github.com/mellybelly">https://github.com/mellybelly</a>, @miguelfortuna <a href="https://github.com/miguelfortuna">https://github.com/miguelfortuna</a>, @mjy <a href="https://github.com/mjy">https://github.com/mjy</a>, @nandadorea <a href="https://github.com/nandadorea">https://github.com/nandadorea</a>, @pbuttigieg <a href="https://github.com/pbuttigieg">https://github.com/pbuttigieg</a>, @pfabry <a href="https://github.com/pfabry">https://github.com/pfabry</a>, @phismith <a href="https://github.com/phismith">https://github.com/phismith</a>, @pporrasebi <a href="https://github.com/pporrasebi">https://github.com/pporrasebi</a>, @ramonawalls <a href="https://github.com/ramonawalls">https://github.com/ramonawalls</a>, @rsmsheriff <a href="https://github.com/rsmsheriff">https://github.com/rsmsheriff</a>, @safisher <a href="https://github.com/safisher">https://github.com/safisher</a>, @sbello <a href="https://github.com/sbello">https://github.com/sbello</a>, @srengel <a href="https://github.com/srengel">https://github.com/srengel</a>, @srobb1 <a href="https://github.com/srobb1">https://github.com/srobb1</a>, @suzialeksander <a href="https://github.com/suzialeksander">https://github.com/suzialeksander</a>, @tfhayamizu <a href="https://github.com/tfhayamizu">https://github.com/tfhayamizu</a>, @wawong <a href="https://github.com/wawong">https://github.com/wawong</a>, @wdduncan <a href="https://github.com/wdduncan">https://github.com/wdduncan</a>, @ybradford <a href="https://github.com/ybradford">https://github.com/ybradford</a>, @yongqunh <a href="https://github.com/yongqunh">https://github.com/yongqunh</a>, @yuki-yamagata <a href="https://github.com/yuki-yamagata">https://github.com/yuki-yamagata</a>, @zachll <a href="https://github.com/zachll">https://github.com/zachll</a>, @zhengj2007 <a href="https://github.com/zhengj2007">https://github.com/zhengj2007</a></p> <p>— Reply to this email directly, view it on GitHub <a href="https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118269687">https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118269687</a>, or unsubscribe <a href="https://github.com/notifications/unsubscribe-auth/AAJR55S6233N2BP4J7AZW7DVIN5HDANCNFSM5S7REGLA">https://github.com/notifications/unsubscribe-auth/AAJR55S6233N2BP4J7AZW7DVIN5HDANCNFSM5S7REGLA</a> . You are receiving this because you were mentioned.Message ID: <strong><em>@</em></strong>.***></p> </blockquote> </div> </div> <div class="comment"> <div class="user"> <a rel="noreferrer nofollow" target="_blank" href="https://github.com/matentzn"><img src="https://avatars.githubusercontent.com/u/7070631?v=4" />matentzn</a> commented <strong> 1 year ago</strong> </div> <div class="markdown-body"> <p>Closing this issue now; some publications have been added in response! Thanks @cthoyt to drive this forward! Hopefully more people will add their preferred publication to make it easier to cite OBO ontologes.</p> </div> </div> <div class="page-bar-simple"> </div> <div class="footer"> <ul class="body"> <li>© <script> document.write(new Date().getFullYear()) </script> Githubissues.</li> <li>Githubissues is a development platform for aggregating issues.</li> </ul> </div> <script src="https://cdn.jsdelivr.net/npm/jquery@3.5.1/dist/jquery.min.js"></script> <script src="/githubissues/assets/js.js"></script> <script src="/githubissues/assets/markdown.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/highlight.min.js"></script> <script src="https://cdn.jsdelivr.net/gh/highlightjs/cdn-release@11.4.0/build/languages/go.min.js"></script> <script> hljs.highlightAll(); </script> </body> </html>
When this issue was opened, 151 active ontologies in the OBO Foundry did not have a
publications:entry in their metadata. This field is used to generate the citation information on the ontology page (see image below with ChEBI as an example)Inside the metadata, this looks like the following, with an
id:field containing a URL based on a PubMed identifier and atitle:that can be free text. Thepublications:field is a list and it's also possible to have multiple entries, each with their ownidandtitle. Here's what the metadata looks like for ChEBI:https://github.com/OBOFoundry/OBOFoundry.github.io/blob/7152dbb4f238d024a37290f971b5e3a8facc54a6/ontology/chebi.md?plain=1#L26-L28
Ontologies Missing Publications
The following is table with all of the ontologies that are missing the
publicationsfield including a tag for the responsible person for each. You can use the following template in your ontology's metadata by replacing<PUBMED>and<TITLE>with your ontology's publication information:There's an "edit" button for each row of the table which will bring you directly to the place where you can edit your ontology's metadata in browser.
Click to see the whole table
Note: we started this effort with almost 160 ontologies missing this information, and now this table has been updated to reflect that we've indeed made progress! | | Prefix | Title | Contact | Edit | |-----|--------------------------------------------------------|----------------------------------------------------------------------------|--------------------|----------------------------------------------------------------------------------------------| | 1 | [aism](https://obofoundry.org/ontology/aism) | Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) | @JCGiron | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/aism.md) | | 2 | [amphx](https://obofoundry.org/ontology/amphx) | The Amphioxus Development and Anatomy Ontology | @hescriva | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/amphx.md) | | 3 | [apo](https://obofoundry.org/ontology/apo) | Ascomycete phenotype ontology | @srengel | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/apo.md) | | 4 | [bco](https://obofoundry.org/ontology/bco) | Biological Collections Ontology | @ramonawalls | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/bco.md) | | 5 | [bfo](https://obofoundry.org/ontology/bfo) | Basic Formal Ontology | @phismith | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/bfo.md) | | 6 | [caro](https://obofoundry.org/ontology/caro) | Common Anatomy Reference Ontology | @mellybelly | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/caro.md) | | 7 | [cdao](https://obofoundry.org/ontology/cdao) | Comparative Data Analysis Ontology | @balhoff | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cdao.md) | | 8 | [cdno](https://obofoundry.org/ontology/cdno) | Compositional Dietary Nutrition Ontology | @LilyAndres | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cdno.md) | | 9 | [chmo](https://obofoundry.org/ontology/chmo) | Chemical Methods Ontology | @batchelorc | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/chmo.md) | | 10 | [cido](https://obofoundry.org/ontology/cido) | Coronavirus Infectious Disease Ontology | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cido.md) | | 11 | [cio](https://obofoundry.org/ontology/cio) | Confidence Information Ontology | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cio.md) | | 12 | [clao](https://obofoundry.org/ontology/clao) | Collembola Anatomy Ontology | @luis-gonzalez-m | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/clao.md) | | 13 | [clyh](https://obofoundry.org/ontology/clyh) | Clytia hemisphaerica Development and Anatomy Ontology | @L-Leclere | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/clyh.md) | | 14 | [cob](https://obofoundry.org/ontology/cob) | Core Ontology for Biology and Biomedicine | @bpeters42 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cob.md) | | 15 | [colao](https://obofoundry.org/ontology/colao) | Coleoptera Anatomy Ontology (COLAO) | @JCGiron | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/colao.md) | | 16 | [cro](https://obofoundry.org/ontology/cro) | Contributor Role Ontology | @marijane | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cro.md) | | 17 | [cteno](https://obofoundry.org/ontology/cteno) | Ctenophore Ontology | @cmungall | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cteno.md) | | 18 | [cto](https://obofoundry.org/ontology/cto) | CTO: Core Ontology of Clinical Trials | @akodamullil | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cto.md) | | 19 | [cvdo](https://obofoundry.org/ontology/cvdo) | Cardiovascular Disease Ontology | @pfabry | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/cvdo.md) | | 20 | [dideo](https://obofoundry.org/ontology/dideo) | Drug-drug Interaction and Drug-drug Interaction Evidence Ontology | @mbrochhausen | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/dideo.md) | | 21 | [disdriv](https://obofoundry.org/ontology/disdriv) | Disease Drivers Ontology | @lschriml | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/disdriv.md) | | 22 | [duo](https://obofoundry.org/ontology/duo) | Data Use Ontology | @mcourtot | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/duo.md) | | 23 | [ecao](https://obofoundry.org/ontology/ecao) | The Echinoderm Anatomy and Development Ontology | @ettensohn | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ecao.md) | | 24 | [ecocore](https://obofoundry.org/ontology/ecocore) | An ontology of core ecological entities | @pbuttigieg | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ecocore.md) | | 25 | [ecto](https://obofoundry.org/ontology/ecto) | Environmental conditions, treatments and exposures ontology | @diatomsRcool | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ecto.md) | | 26 | [emapa](https://obofoundry.org/ontology/emapa) | Mouse Developmental Anatomy Ontology | @tfhayamizu | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/emapa.md) | | 27 | [epio](https://obofoundry.org/ontology/epio) | Epilepsy Ontology | @akodamullil | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/epio.md) | | 28 | [eupath](https://obofoundry.org/ontology/eupath) | VEuPathDB ontology | @cstoeckert | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/eupath.md) | | 29 | [exo](https://obofoundry.org/ontology/exo) | Exposure ontology | @diatomsRcool | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/exo.md) | | 30 | [fao](https://obofoundry.org/ontology/fao) | Fungal gross anatomy | @ValWood | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fao.md) | | 31 | [fbbi](https://obofoundry.org/ontology/fbbi) | Biological Imaging Methods Ontology | @wawong | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fbbi.md) | | 32 | [fbcv](https://obofoundry.org/ontology/fbcv) | FlyBase Controlled Vocabulary | @Clare72 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fbcv.md) | | 33 | [fbdv](https://obofoundry.org/ontology/fbdv) | Drosophila development | @Clare72 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fbdv.md) | | 34 | [fideo](https://obofoundry.org/ontology/fideo) | Food Interactions with Drugs Evidence Ontology | @getbordea | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fideo.md) | | 35 | [flopo](https://obofoundry.org/ontology/flopo) | Flora Phenotype Ontology | @leechuck | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/flopo.md) | | 36 | [foodon](https://obofoundry.org/ontology/foodon) | Food Ontology | @ddooley | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/foodon.md) | | 37 | [fovt](https://obofoundry.org/ontology/fovt) | FuTRES Ontology of Vertebrate Traits | @megbalk | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/fovt.md) | | 38 | [gecko](https://obofoundry.org/ontology/gecko) | Genomics Cohorts Knowledge Ontology | @beckyjackson | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/gecko.md) | | 39 | [genepio](https://obofoundry.org/ontology/genepio) | Genomic Epidemiology Ontology | @ddooley | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/genepio.md) | | 40 | [geno](https://obofoundry.org/ontology/geno) | Genotype Ontology | @mbrush | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/geno.md) | | 41 | [geo](https://obofoundry.org/ontology/geo) | Geographical Entity Ontology | @hoganwr | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/geo.md) | | 42 | [gno](https://obofoundry.org/ontology/gno) | Glycan Naming and Subsumption Ontology (GNOme) | @edwardsnj | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/gno.md) | | 43 | [go](https://obofoundry.org/ontology/go) | Gene Ontology | @suzialeksander | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/go.md) | | 44 | [gsso](https://obofoundry.org/ontology/gsso) | Gender, Sex, and Sexual Orientation (GSSO) ontology | @Superraptor | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/gsso.md) | | 45 | [hancestro](https://obofoundry.org/ontology/hancestro) | Human Ancestry Ontology | @daniwelter | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/hancestro.md) | | 46 | [hom](https://obofoundry.org/ontology/hom) | Homology Ontology | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/hom.md) | | 47 | [hsapdv](https://obofoundry.org/ontology/hsapdv) | Human Developmental Stages | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/hsapdv.md) | | 48 | [hso](https://obofoundry.org/ontology/hso) | Health Surveillance Ontology | @nandadorea | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/hso.md) | | 49 | [htn](https://obofoundry.org/ontology/htn) | Hypertension Ontology | @aellenhicks | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/htn.md) | | 50 | [iao](https://obofoundry.org/ontology/iao) | Information Artifact Ontology | @zhengj2007 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/iao.md) | | 51 | [iceo](https://obofoundry.org/ontology/iceo) | Integrative and Conjugative Element Ontology | @Lemon-Liu | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/iceo.md) | | 52 | [ico](https://obofoundry.org/ontology/ico) | Informed Consent Ontology | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ico.md) | | 53 | [ido](https://obofoundry.org/ontology/ido) | Infectious Disease Ontology | @lgcowell | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ido.md) | | 54 | [ino](https://obofoundry.org/ontology/ino) | Interaction Network Ontology | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ino.md) | | 55 | [kisao](https://obofoundry.org/ontology/kisao) | Kinetic Simulation Algorithm Ontology | @jonrkarr | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/kisao.md) | | 56 | [labo](https://obofoundry.org/ontology/labo) | clinical LABoratory Ontology | @pfabry | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/labo.md) | | 57 | [lepao](https://obofoundry.org/ontology/lepao) | Lepidoptera Anatomy Ontology | @luis-gonzalez-m | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/lepao.md) | | 58 | [ma](https://obofoundry.org/ontology/ma) | Mouse adult gross anatomy | @tfhayamizu | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ma.md) | | 59 | [mamo](https://obofoundry.org/ontology/mamo) | Mathematical modeling ontology | @gambardella | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mamo.md) | | 60 | [maxo](https://obofoundry.org/ontology/maxo) | Medical Action Ontology | @LCCarmody | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/maxo.md) | | 61 | [mco](https://obofoundry.org/ontology/mco) | Microbial Conditions Ontology | @citmejia | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mco.md) | | 62 | [mf](https://obofoundry.org/ontology/mf) | Mental Functioning Ontology | @jannahastings | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mf.md) | | 63 | [mfmo](https://obofoundry.org/ontology/mfmo) | Mammalian Feeding Muscle Ontology | @RDruzinsky | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mfmo.md) | | 64 | [mfoem](https://obofoundry.org/ontology/mfoem) | Emotion Ontology | @jannahastings | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mfoem.md) | | 65 | [mfomd](https://obofoundry.org/ontology/mfomd) | Mental Disease Ontology | @jannahastings | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mfomd.md) | | 66 | [mi](https://obofoundry.org/ontology/mi) | Molecular Interactions Controlled Vocabulary | @pporrasebi | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mi.md) | | 67 | [miapa](https://obofoundry.org/ontology/miapa) | MIAPA Ontology | @hlapp | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/miapa.md) | | 68 | [micro](https://obofoundry.org/ontology/micro) | Ontology of Prokaryotic Phenotypic and Metabolic Characters | @carrineblank | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/micro.md) | | 69 | [mmusdv](https://obofoundry.org/ontology/mmusdv) | Mouse Developmental Stages | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mmusdv.md) | | 70 | [mop](https://obofoundry.org/ontology/mop) | Molecular Process Ontology | @batchelorc | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mop.md) | | 71 | [mp](https://obofoundry.org/ontology/mp) | Mammalian Phenotype Ontology | @sbello | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mp.md) | | 72 | [mpath](https://obofoundry.org/ontology/mpath) | Mouse pathology ontology | @PaulNSchofield | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mpath.md) | | 73 | [mpio](https://obofoundry.org/ontology/mpio) | Minimum PDDI Information Ontology | @mbrochhausen | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mpio.md) | | 74 | [mro](https://obofoundry.org/ontology/mro) | MHC Restriction Ontology | @bpeters42 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/mro.md) | | 75 | [ncbitaxon](https://obofoundry.org/ontology/ncbitaxon) | NCBI organismal classification | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ncbitaxon.md) | | 76 | [ncit](https://obofoundry.org/ontology/ncit) | NCI Thesaurus OBO Edition | @mellybelly | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ncit.md) | | 77 | [ncro](https://obofoundry.org/ontology/ncro) | Non-Coding RNA Ontology | @Huang-OMIT | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ncro.md) | | 78 | [nomen](https://obofoundry.org/ontology/nomen) | NOMEN - A nomenclatural ontology for biological names | @mjy | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/nomen.md) | | 79 | [oae](https://obofoundry.org/ontology/oae) | Ontology of Adverse Events | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/oae.md) | | 80 | [oarcs](https://obofoundry.org/ontology/oarcs) | Ontology of Arthropod Circulatory Systems | @mjy | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/oarcs.md) | | 81 | [oba](https://obofoundry.org/ontology/oba) | Ontology of Biological Attributes | @cmungall | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/oba.md) | | 82 | [obcs](https://obofoundry.org/ontology/obcs) | Ontology of Biological and Clinical Statistics | @zhengj2007 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/obcs.md) | | 83 | [obib](https://obofoundry.org/ontology/obib) | Ontology for Biobanking | @zhengj2007 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/obib.md) | | 84 | [ogg](https://obofoundry.org/ontology/ogg) | The Ontology of Genes and Genomes | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ogg.md) | | 85 | [ogms](https://obofoundry.org/ontology/ogms) | Ontology for General Medical Science | @BAevermann | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ogms.md) | | 86 | [ogsf](https://obofoundry.org/ontology/ogsf) | Ontology of Genetic Susceptibility Factor | @linikujp | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ogsf.md) | | 87 | [ohd](https://obofoundry.org/ontology/ohd) | Oral Health and Disease Ontology | @wdduncan | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ohd.md) | | 88 | [ohmi](https://obofoundry.org/ontology/ohmi) | Ontology of Host-Microbiome Interactions | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ohmi.md) | | 89 | [ohpi](https://obofoundry.org/ontology/ohpi) | Ontology of Host Pathogen Interactions | @e4ong1031 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ohpi.md) | | 90 | [olatdv](https://obofoundry.org/ontology/olatdv) | Medaka Developmental Stages | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/olatdv.md) | | 91 | [omit](https://obofoundry.org/ontology/omit) | Ontology for MIRNA Target | @Huang-OMIT | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/omit.md) | | 92 | [omo](https://obofoundry.org/ontology/omo) | OBO Metadata Ontology | @cmungall | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/omo.md) | | 93 | [omp](https://obofoundry.org/ontology/omp) | Ontology of Microbial Phenotypes | @jimhu-tamu | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/omp.md) | | 94 | [one](https://obofoundry.org/ontology/one) | Ontology for Nutritional Epidemiology | @cyang0128 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/one.md) | | 95 | [ons](https://obofoundry.org/ontology/ons) | Ontology for Nutritional Studies | @FrancescoVit | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ons.md) | | 96 | [ontoavida](https://obofoundry.org/ontology/ontoavida) | OntoAvida: ontology for Avida digital evolution platform | @miguelfortuna | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ontoavida.md) | | 97 | [ontoneo](https://obofoundry.org/ontology/ontoneo) | Obstetric and Neonatal Ontology | @FernandaFarinelli | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ontoneo.md) | | 98 | [oostt](https://obofoundry.org/ontology/oostt) | Ontology of Organizational Structures of Trauma centers and Trauma systems | @mbrochhausen | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/oostt.md) | | 99 | [opl](https://obofoundry.org/ontology/opl) | Ontology for Parasite LifeCycle | @zhengj2007 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/opl.md) | | 100 | [opmi](https://obofoundry.org/ontology/opmi) | Ontology of Precision Medicine and Investigation | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/opmi.md) | | 101 | [ornaseq](https://obofoundry.org/ontology/ornaseq) | Ontology of RNA Sequencing | @safisher | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ornaseq.md) | | 102 | [ovae](https://obofoundry.org/ontology/ovae) | Ontology of Vaccine Adverse Events | @yongqunh | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ovae.md) | | 103 | [pcl](https://obofoundry.org/ontology/pcl) | Provisional Cell Ontology | @dosumis | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/pcl.md) | | 104 | [pco](https://obofoundry.org/ontology/pco) | Population and Community Ontology | @ramonawalls | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/pco.md) | | 105 | [pdro](https://obofoundry.org/ontology/pdro) | The Prescription of Drugs Ontology | @pfabry | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/pdro.md) | | 106 | [pdumdv](https://obofoundry.org/ontology/pdumdv) | Platynereis Developmental Stages | @fbastian | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/pdumdv.md) | | 107 | [phipo](https://obofoundry.org/ontology/phipo) | Pathogen Host Interaction Phenotype Ontology | @CuzickA | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/phipo.md) | | 108 | [plana](https://obofoundry.org/ontology/plana) | planaria-ontology | @srobb1 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/plana.md) | | 109 | [planp](https://obofoundry.org/ontology/planp) | Planarian Phenotype Ontology | @srobb1 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/planp.md) | | 110 | [ppo](https://obofoundry.org/ontology/ppo) | Plant Phenology Ontology | @ramonawalls | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ppo.md) | | 111 | [psdo](https://obofoundry.org/ontology/psdo) | Performance Summary Display Ontology | @zachll | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/psdo.md) | | 112 | [pso](https://obofoundry.org/ontology/pso) | Plant Stress Ontology | @cooperl09 | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/pso.md) | | 113 | [rbo](https://obofoundry.org/ontology/rbo) | Radiation Biology Ontology | @DanBerrios | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/rbo.md) | | 114 | [ro](https://obofoundry.org/ontology/ro) | Relation Ontology | @cmungall | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/ro.md) | | 115 | [rxno](https://obofoundry.org/ontology/rxno) | Name Reaction Ontology | @batchelorc | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/rxno.md) | | 116 | [sbo](https://obofoundry.org/ontology/sbo) | Systems Biology Ontology | @rsmsheriff | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/sbo.md) | | 117 | [scdo](https://obofoundry.org/ontology/scdo) | Sickle Cell Disease Ontology | @JadeHotchkiss | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/scdo.md) | | 118 | [sepio](https://obofoundry.org/ontology/sepio) | Scientific Evidence and Provenance Information Ontology | @mbrush | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/sepio.md) | | 119 | [spd](https://obofoundry.org/ontology/spd) | Spider Ontology | @martinjramirez | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/spd.md) | | 120 | [stato](https://obofoundry.org/ontology/stato) | The Statistical Methods Ontology | @agbeltran | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/stato.md) | | 121 | [swo](https://obofoundry.org/ontology/swo) | Software ontology | @allysonlister | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/swo.md) | | 122 | [symp](https://obofoundry.org/ontology/symp) | Symptom Ontology | @lschriml | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/symp.md) | | 123 | [taxrank](https://obofoundry.org/ontology/taxrank) | Taxonomic rank vocabulary | @balhoff | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/taxrank.md) | | 124 | [trans](https://obofoundry.org/ontology/trans) | Pathogen Transmission Ontology | @lschriml | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/trans.md) | | 125 | [tto](https://obofoundry.org/ontology/tto) | Teleost taxonomy ontology | @balhoff | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/tto.md) | | 126 | [txpo](https://obofoundry.org/ontology/txpo) | Toxic Process Ontology | @yuki-yamagata | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/txpo.md) | | 127 | [vt](https://obofoundry.org/ontology/vt) | Vertebrate trait ontology | @caripark | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/vt.md) | | 128 | [vto](https://obofoundry.org/ontology/vto) | Vertebrate Taxonomy Ontology | @balhoff | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/vto.md) | | 129 | [xlmod](https://obofoundry.org/ontology/xlmod) | HUPO-PSI cross-linking and derivatization reagents controlled vocabulary | @lutzfischer | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/xlmod.md) | | 130 | [zeco](https://obofoundry.org/ontology/zeco) | Zebrafish Experimental Conditions Ontology | @ybradford | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/zeco.md) | | 131 | [zfs](https://obofoundry.org/ontology/zfs) | Zebrafish developmental stages ontology | @cerivs | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/zfs.md) | | 132 | [zp](https://obofoundry.org/ontology/zp) | Zebrafish Phenotype Ontology | @ybradford | [edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/zp.md) |Code
The code that was used to generate this table
```python from textwrap import wrap from bioregistry.external.obofoundry import get_obofoundry from tabulate import tabulate from more_itertools import chunked def main(): pre_rows = [ (prefix, data) for prefix, data in sorted(get_obofoundry(force_download=True).items()) if ( not data.get("inactive") and not data.get("deprecated") and not data.get("publications") ) ] rows = [ ( i, f"[{prefix}](https://obofoundry.org/ontology/{prefix})", data["name"], f"@{data['contact.github']}", f"[edit](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/{prefix}.md)", ) for i, (prefix, data) in enumerate(pre_rows, start=1) ] print( tabulate( rows, headers=["", "Prefix", "Title", "Contact", "Edit"], tablefmt="github", ) ) githubs = sorted({f"@{data['contact.github']}" for _, data in pre_rows}) print(f"\n\nThere are {len(githubs):,} GitHub accounts:") for i, group in enumerate(chunked(githubs, 45), start=1): print(f"Group {i}") print("\n".join(wrap(", ".join(group)))) print() if __name__ == "__main__": main() ```See Also
After we started making updates, we had a lot of interesting discussions about what kinds of "identifiers" would be useful and/or allowed. See also https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1846, https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1859.