Call to add publications to ontology metadata

[cthoyt]

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 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:

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 publications field 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:

 publications: 
   - id: https://www.ncbi.nlm.nih.gov/pubmed/<PUBMED>
     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.

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	Ontology for the Anatomy of the Insect SkeletoMuscular system (AISM)	@JCGiron	edit
2	amphx	The Amphioxus Development and Anatomy Ontology	@hescriva	edit
3	apo	Ascomycete phenotype ontology	@srengel	edit
4	bco	Biological Collections Ontology	@ramonawalls	edit
5	bfo	Basic Formal Ontology	@phismith	edit
6	caro	Common Anatomy Reference Ontology	@mellybelly	edit
7	cdao	Comparative Data Analysis Ontology	@balhoff	edit
8	cdno	Compositional Dietary Nutrition Ontology	@LilyAndres	edit
9	chmo	Chemical Methods Ontology	@batchelorc	edit
10	cido	Coronavirus Infectious Disease Ontology	@yongqunh	edit
11	cio	Confidence Information Ontology	@fbastian	edit
12	clao	Collembola Anatomy Ontology	@luis-gonzalez-m	edit
13	clyh	Clytia hemisphaerica Development and Anatomy Ontology	@L-Leclere	edit
14	cob	Core Ontology for Biology and Biomedicine	@bpeters42	edit
15	colao	Coleoptera Anatomy Ontology (COLAO)	@JCGiron	edit
16	cro	Contributor Role Ontology	@marijane	edit
17	cteno	Ctenophore Ontology	@cmungall	edit
18	cto	CTO: Core Ontology of Clinical Trials	@akodamullil	edit
19	cvdo	Cardiovascular Disease Ontology	@pfabry	edit
20	dideo	Drug-drug Interaction and Drug-drug Interaction Evidence Ontology	@mbrochhausen	edit
21	disdriv	Disease Drivers Ontology	@lschriml	edit
22	duo	Data Use Ontology	@mcourtot	edit
23	ecao	The Echinoderm Anatomy and Development Ontology	@ettensohn	edit
24	ecocore	An ontology of core ecological entities	@pbuttigieg	edit
25	ecto	Environmental conditions, treatments and exposures ontology	@diatomsRcool	edit
26	emapa	Mouse Developmental Anatomy Ontology	@tfhayamizu	edit
27	epio	Epilepsy Ontology	@akodamullil	edit
28	eupath	VEuPathDB ontology	@cstoeckert	edit
29	exo	Exposure ontology	@diatomsRcool	edit
30	fao	Fungal gross anatomy	@ValWood	edit
31	fbbi	Biological Imaging Methods Ontology	@wawong	edit
32	fbcv	FlyBase Controlled Vocabulary	@Clare72	edit
33	fbdv	Drosophila development	@Clare72	edit
34	fideo	Food Interactions with Drugs Evidence Ontology	@getbordea	edit
35	flopo	Flora Phenotype Ontology	@leechuck	edit
36	foodon	Food Ontology	@ddooley	edit
37	fovt	FuTRES Ontology of Vertebrate Traits	@megbalk	edit
38	gecko	Genomics Cohorts Knowledge Ontology	@beckyjackson	edit
39	genepio	Genomic Epidemiology Ontology	@ddooley	edit
40	geno	Genotype Ontology	@mbrush	edit
41	geo	Geographical Entity Ontology	@hoganwr	edit
42	gno	Glycan Naming and Subsumption Ontology (GNOme)	@edwardsnj	edit
43	go	Gene Ontology	@suzialeksander	edit
44	gsso	Gender, Sex, and Sexual Orientation (GSSO) ontology	@Superraptor	edit
45	hancestro	Human Ancestry Ontology	@daniwelter	edit
46	hom	Homology Ontology	@fbastian	edit
47	hsapdv	Human Developmental Stages	@fbastian	edit
48	hso	Health Surveillance Ontology	@nandadorea	edit
49	htn	Hypertension Ontology	@aellenhicks	edit
50	iao	Information Artifact Ontology	@zhengj2007	edit
51	iceo	Integrative and Conjugative Element Ontology	@Lemon-Liu	edit
52	ico	Informed Consent Ontology	@yongqunh	edit
53	ido	Infectious Disease Ontology	@lgcowell	edit
54	ino	Interaction Network Ontology	@yongqunh	edit
55	kisao	Kinetic Simulation Algorithm Ontology	@jonrkarr	edit
56	labo	clinical LABoratory Ontology	@pfabry	edit
57	lepao	Lepidoptera Anatomy Ontology	@luis-gonzalez-m	edit
58	ma	Mouse adult gross anatomy	@tfhayamizu	edit
59	mamo	Mathematical modeling ontology	@gambardella	edit
60	maxo	Medical Action Ontology	@LCCarmody	edit
61	mco	Microbial Conditions Ontology	@citmejia	edit
62	mf	Mental Functioning Ontology	@jannahastings	edit
63	mfmo	Mammalian Feeding Muscle Ontology	@RDruzinsky	edit
64	mfoem	Emotion Ontology	@jannahastings	edit
65	mfomd	Mental Disease Ontology	@jannahastings	edit
66	mi	Molecular Interactions Controlled Vocabulary	@pporrasebi	edit
67	miapa	MIAPA Ontology	@hlapp	edit
68	micro	Ontology of Prokaryotic Phenotypic and Metabolic Characters	@carrineblank	edit
69	mmusdv	Mouse Developmental Stages	@fbastian	edit
70	mop	Molecular Process Ontology	@batchelorc	edit
71	mp	Mammalian Phenotype Ontology	@sbello	edit
72	mpath	Mouse pathology ontology	@PaulNSchofield	edit
73	mpio	Minimum PDDI Information Ontology	@mbrochhausen	edit
74	mro	MHC Restriction Ontology	@bpeters42	edit
75	ncbitaxon	NCBI organismal classification	@fbastian	edit
76	ncit	NCI Thesaurus OBO Edition	@mellybelly	edit
77	ncro	Non-Coding RNA Ontology	@Huang-OMIT	edit
78	nomen	NOMEN - A nomenclatural ontology for biological names	@mjy	edit
79	oae	Ontology of Adverse Events	@yongqunh	edit
80	oarcs	Ontology of Arthropod Circulatory Systems	@mjy	edit
81	oba	Ontology of Biological Attributes	@cmungall	edit
82	obcs	Ontology of Biological and Clinical Statistics	@zhengj2007	edit
83	obib	Ontology for Biobanking	@zhengj2007	edit
84	ogg	The Ontology of Genes and Genomes	@yongqunh	edit
85	ogms	Ontology for General Medical Science	@BAevermann	edit
86	ogsf	Ontology of Genetic Susceptibility Factor	@linikujp	edit
87	ohd	Oral Health and Disease Ontology	@wdduncan	edit
88	ohmi	Ontology of Host-Microbiome Interactions	@yongqunh	edit
89	ohpi	Ontology of Host Pathogen Interactions	@e4ong1031	edit
90	olatdv	Medaka Developmental Stages	@fbastian	edit
91	omit	Ontology for MIRNA Target	@Huang-OMIT	edit
92	omo	OBO Metadata Ontology	@cmungall	edit
93	omp	Ontology of Microbial Phenotypes	@jimhu-tamu	edit
94	one	Ontology for Nutritional Epidemiology	@cyang0128	edit
95	ons	Ontology for Nutritional Studies	@FrancescoVit	edit
96	ontoavida	OntoAvida: ontology for Avida digital evolution platform	@miguelfortuna	edit
97	ontoneo	Obstetric and Neonatal Ontology	@FernandaFarinelli	edit
98	oostt	Ontology of Organizational Structures of Trauma centers and Trauma systems	@mbrochhausen	edit
99	opl	Ontology for Parasite LifeCycle	@zhengj2007	edit
100	opmi	Ontology of Precision Medicine and Investigation	@yongqunh	edit
101	ornaseq	Ontology of RNA Sequencing	@safisher	edit
102	ovae	Ontology of Vaccine Adverse Events	@yongqunh	edit
103	pcl	Provisional Cell Ontology	@dosumis	edit
104	pco	Population and Community Ontology	@ramonawalls	edit
105	pdro	The Prescription of Drugs Ontology	@pfabry	edit
106	pdumdv	Platynereis Developmental Stages	@fbastian	edit
107	phipo	Pathogen Host Interaction Phenotype Ontology	@CuzickA	edit
108	plana	planaria-ontology	@srobb1	edit
109	planp	Planarian Phenotype Ontology	@srobb1	edit
110	ppo	Plant Phenology Ontology	@ramonawalls	edit
111	psdo	Performance Summary Display Ontology	@zachll	edit
112	pso	Plant Stress Ontology	@cooperl09	edit
113	rbo	Radiation Biology Ontology	@DanBerrios	edit
114	ro	Relation Ontology	@cmungall	edit
115	rxno	Name Reaction Ontology	@batchelorc	edit
116	sbo	Systems Biology Ontology	@rsmsheriff	edit
117	scdo	Sickle Cell Disease Ontology	@JadeHotchkiss	edit
118	sepio	Scientific Evidence and Provenance Information Ontology	@mbrush	edit
119	spd	Spider Ontology	@martinjramirez	edit
120	stato	The Statistical Methods Ontology	@agbeltran	edit
121	swo	Software ontology	@allysonlister	edit
122	symp	Symptom Ontology	@lschriml	edit
123	taxrank	Taxonomic rank vocabulary	@balhoff	edit
124	trans	Pathogen Transmission Ontology	@lschriml	edit
125	tto	Teleost taxonomy ontology	@balhoff	edit
126	txpo	Toxic Process Ontology	@yuki-yamagata	edit
127	vt	Vertebrate trait ontology	@caripark	edit
128	vto	Vertebrate Taxonomy Ontology	@balhoff	edit
129	xlmod	HUPO-PSI cross-linking and derivatization reagents controlled vocabulary	@lutzfischer	edit
130	zeco	Zebrafish Experimental Conditions Ontology	@ybradford	edit
131	zfs	Zebrafish developmental stages ontology	@cerivs	edit
132	zp	Zebrafish Phenotype Ontology	@ybradford	edit

Code

The code that was used to generate this table

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.

[nicolevasilevsky]

@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]

@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]

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]

@cthoyt my bad, it was me, not you. :) Thanks for clarifying.

[gkoutos]

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:

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 publications field 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:

publications :

id: https://www.ncbi.nlm.nih.gov/pubmed/<PUBMED>

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.

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

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.

[pfey03]

Hello Charles, For Dicty ontologies please use these papers

DDANAT use PMID: 18366659 DDPHENO use PMID: 31840793

Many thanks, Petra

[cthoyt]

Ping to the following responsible contacts, who might not have got a notification because of the apparent 45-tag maximum in an issue:

@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

[cthoyt]

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:

@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

[LCCarmody]

There isn't a primary article foR MAxO (it is in preparation). Only papers referring to collaborations. Do you want these, too?

[ettensohn]

Please remove me from this email chain!!!!

On Thu, May 5, 2022 at 3:55 AM Charles Tapley Hoyt @.***> wrote:

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:

@hoganwr https://github.com/hoganwr, @jannahastings https://github.com/jannahastings, @jimhu-tamu https://github.com/jimhu-tamu, @jonrkarr https://github.com/jonrkarr, @leechuck https://github.com/leechuck, @lgcowell https://github.com/lgcowell, @linikujp https://github.com/linikujp, @lschriml https://github.com/lschriml, @luis-gonzalez-m https://github.com/luis-gonzalez-m, @lutzfischer https://github.com/lutzfischer, @marijane https://github.com/marijane, @martinjramirez https://github.com/martinjramirez, @mbrochhausen https://github.com/mbrochhausen, @mbrush https://github.com/mbrush, @mcourtot https://github.com/mcourtot, @megbalk https://github.com/megbalk, @mellybelly https://github.com/mellybelly, @miguelfortuna https://github.com/miguelfortuna, @mjy https://github.com/mjy, @nandadorea https://github.com/nandadorea, @pbuttigieg https://github.com/pbuttigieg, @pfabry https://github.com/pfabry, @phismith https://github.com/phismith, @pporrasebi https://github.com/pporrasebi, @ramonawalls https://github.com/ramonawalls, @rsmsheriff https://github.com/rsmsheriff, @safisher https://github.com/safisher, @sbello https://github.com/sbello, @srengel https://github.com/srengel, @srobb1 https://github.com/srobb1, @suzialeksander https://github.com/suzialeksander, @tfhayamizu https://github.com/tfhayamizu, @wawong https://github.com/wawong, @wdduncan https://github.com/wdduncan, @ybradford https://github.com/ybradford, @yongqunh https://github.com/yongqunh, @yuki-yamagata https://github.com/yuki-yamagata, @zachll https://github.com/zachll, @zhengj2007 https://github.com/zhengj2007

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-- Dr. Charles A. Ettensohn Professor of Biological Sciences Carnegie Mellon University Tel: 412-268-5849 Email: @.***

[cthoyt]

@ettensohn you're listed as the contact person for ECAO https://obofoundry.org/ontology/ecao, 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"?

[tfhayamizu]

Don't know why I received this email. Appears I was cc'd. I have no association with the echinoderm anatomy ontology.

Terry

On 5/5/22, 9:51 AM, Charles Tapley Hoyt @.@.>> wrote:

@ettensohnhttps://github.com/ettensohn you're listed as the contact person for ECAO https://obofoundry.org/ontology/ecao, 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?

— Reply to this email directly, view it on GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118580912, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAG7BKJCHMMIL7WTXKFDSETVIPG6VANCNFSM5S7REGLA. You are receiving this because you were mentioned.Message ID: @.***>

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.

[lschriml]

Thank you @cthoyt - the Human Disease Ontology already has two publications included. Cheers, Lynn

[cthoyt]

@tfhayamizu you're listed as the contact for MA and EMAPA, 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?

[cthoyt]

@lschriml you're also listed as responsible for disdriv, trans, and symp

[batchelorc]

No publications as yet, sorry.

[JadeHotchkiss]

Updated SCDO #1894

[hlapp]

No publications. (And @cthoyt please remove me being tagged, assuming the purpose of tagging was a ping, not a forced CC on every future comment on this ticket?)

[cthoyt]

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 - https://docs.github.com/en/account-and-profile/managing-subscriptions-and-notifications-on-github/managing-subscriptions-for-activity-on-github/managing-your-subscriptions)

[tfhayamizu]

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.

For the EMAPA:

1. 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.
2. 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.
3. Hayamizu TF, Baldock RA, Ringwald M (2015). Mouse Anatomy Ontologies: Enhancements and Tools for Exploring and Integrating Biomedical Data. Mamm Genome 26, 422-30.

[lschriml]

@cthoyt - yes I am the PI for : disdriv, trans, and symp - I have not added a publication to their ontologies yet

[LilyAndres]

Hello,

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:

homepage: https://cdno.info/ publications:

• id: https://doi.org/10.1002/csc2.20092 title: "<Knowledge representation and data sharing to unlock crop variation for nutritional food security>"

Please let me know if you have any issues with it.

Regards,

Lili

Liliana Andres Hernandez, PhD

Southern Cross Plant Science | Southern Cross University | PO Box 157 | LISMORE NSW 2480, AUSTRALIA

[scps_new_std] [cid:282cca04-9b87-4cf0-8b32-f9fba8139b88]

E: @.*** W: https://github.com/LilyAndres

I acknowledge the Bundjalung people as traditional owners and custodians of the land on which I work and live.

---

From: lschriml @.> Sent: Friday, 6 May 2022 3:38 AM To: OBOFoundry/OBOFoundry.github.io @.> Cc: Liliana Andres Hernandez @.>; Mention @.> Subject: Re: [OBOFoundry/OBOFoundry.github.io] Call to add publications to ontology metadata (Issue #1826)

@cthoythttps://github.com/cthoyt - yes I am the PI for : disdriv, trans, and symp

• I have not added a publication to their ontologies yet

— Reply to this email directly, view it on GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA. You are receiving this because you were mentioned.Message ID: @.***>

[yuki-yamagata]

Hi @cthoyt

Could you add the paper?

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

I appreciate your support!

Yuki

[Clare72]

No pubs for FBdv and FBcv (there is one for dpo, which is incorporated into FBcv, but this is already linked to dpo).

[martinjramirez]

Hello,

I am not sure of this email chain, but we have this publication for SPD:

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. https://doi.org/10.3390/d11100202

Best wishes,

Martin Ramirez

At 21:55 5/5/2022, Liliana Andres wrote:

Hello,

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:

homepage: https://cdno.info/ publications:

• id: https://doi.org/10.1002/csc2.20092 title: "<Knowledge representation and data sharing to unlock crop variation for nutritional food security>"

Please let me know if you have any issues with it.

Regards,

Lili

Liliana Andres Hernandez, PhD

Southern Cross Plant Science | Southern Cross University | PO Box 157 | LISMORE NSW 2480, AUSTRALIA

[scps_new_std] [cid:282cca04-9b87-4cf0-8b32-f9fba8139b88]

E: @.*** W: https://github.com/LilyAndres

I acknowledge the Bundjalung people as traditional owners and custodians of the land on which I work and live.

---

From: lschriml @.> Sent: Friday, 6 May 2022 3:38 AM To: OBOFoundry/OBOFoundry.github.io @.> Cc: Liliana Andres Hernandez @.>; Mention @.> Subject: Re: [OBOFoundry/OBOFoundry.github.io] Call to add publications to ontology metadata (Issue #1826)

@.***https://github.com/cthoyt - yes I am

the PI for : disdriv, trans, and symp

• I have not added a publication to their ontologies yet

— Reply to this email directly, view it on GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118869187, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AGAMGHI4QBMPX5OFQ3JVCJDVIQBP5ANCNFSM5S7REGLA. You are receiving this because you were mentioned.Message ID: @.***>

­ Reply to this email directly, https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1119171442view it on GitHub, or https://github.com/notifications/unsubscribe-auth/AF6DQIBJXCNSRAEOHAVC6ATVIRUZ3ANCNFSM5S7REGLAunsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[suzialeksander]

@cthoyt can you add the following two publications for GO:

Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. May 2000;25(1):25-9. [abstract | full text] The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. Jan 2021;49(D1):D325-D334. [abstract | full text]

thanks

[srengel]

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]

[CuzickA]

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

[wdduncan]

Added citation for the OHD.
https://github.com/OBOFoundry/OBOFoundry.github.io/pull/2102

[hoganwr]

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).

On Thu, May 5, 2022 at 3:55 AM Charles Tapley Hoyt @.***> wrote:

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:

@hoganwr https://github.com/hoganwr, @jannahastings https://github.com/jannahastings, @jimhu-tamu https://github.com/jimhu-tamu, @jonrkarr https://github.com/jonrkarr, @leechuck https://github.com/leechuck, @lgcowell https://github.com/lgcowell, @linikujp https://github.com/linikujp, @lschriml https://github.com/lschriml, @luis-gonzalez-m https://github.com/luis-gonzalez-m, @lutzfischer https://github.com/lutzfischer, @marijane https://github.com/marijane, @martinjramirez https://github.com/martinjramirez, @mbrochhausen https://github.com/mbrochhausen, @mbrush https://github.com/mbrush, @mcourtot https://github.com/mcourtot, @megbalk https://github.com/megbalk, @mellybelly https://github.com/mellybelly, @miguelfortuna https://github.com/miguelfortuna, @mjy https://github.com/mjy, @nandadorea https://github.com/nandadorea, @pbuttigieg https://github.com/pbuttigieg, @pfabry https://github.com/pfabry, @phismith https://github.com/phismith, @pporrasebi https://github.com/pporrasebi, @ramonawalls https://github.com/ramonawalls, @rsmsheriff https://github.com/rsmsheriff, @safisher https://github.com/safisher, @sbello https://github.com/sbello, @srengel https://github.com/srengel, @srobb1 https://github.com/srobb1, @suzialeksander https://github.com/suzialeksander, @tfhayamizu https://github.com/tfhayamizu, @wawong https://github.com/wawong, @wdduncan https://github.com/wdduncan, @ybradford https://github.com/ybradford, @yongqunh https://github.com/yongqunh, @yuki-yamagata https://github.com/yuki-yamagata, @zachll https://github.com/zachll, @zhengj2007 https://github.com/zhengj2007

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1826#issuecomment-1118269687, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJR55S6233N2BP4J7AZW7DVIN5HDANCNFSM5S7REGLA . You are receiving this because you were mentioned.Message ID: @.***>