Request for new ontology [Space LIfe Sciences Ontology]

[DanBerrios]

Title

Space Life Sciences Ontology

Short Description

The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data.

Description

The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA's Life Sciences Data Archive and other systems that contain space life science research data. Many kinds of scientific research in space involve specialized equipment, experimental procedures, specimens and specimen collection apparatus, supporting operational structures, and references to specific space environments and their characteristics. Often such research is extremely costly compared with planetary/terrestrial investigations, and the community supporting space life sciences is accustomed to the use of various specialized concepts and terminologies when dealing with this kind of research and data. However, the underlying conceptual models (and especially the specific labeled relationships in these models) have never been made explicit. The SLSO attempts to provide definition and organization of these models for the space research community.
The SLSO was developed ab inicio using the Ontology Development Kit and imports an extends many concepts from the Basic Formal Ontology (BFO), the Ontology of Biomedical Investigations (OBI), the Environmental Ontology (ENVO), and other OBO Foundry ontologies. Projects at NASA such as the Open Science Data Repository (https://osdr.nasa.gov/) are already using many OBO ontologies, including the Radiation Biology Ontology (https://github.com/Radiobiology-Informatics-Consortium/RBO) and OBI, to index space biology investigation data. With the development of the SLSO, this practice can be extended to include all life science research in space or addressing space effects. Furthermore, the SLSO has a component that imports concepts from the Science Data Discovery Ontology, which was developed to support NASA's Science Discovery Engine (https://sciencediscoveryengine.nasa.gov). These links in the imported SDDO to concepts underlying a broad spectrum of space research (astrophysics, heliophysics, etc.) can ultimately be used to provide key capabilities for discovering and analyzing space life science data and how they relate to other kinds of scientific data regarding space environments.

Identifier Space

SLSO

License

CC-BY 3.0

Domain

investigations

Source Code Repository

https://github.com/nasa/LSDAO

Homepage

https://github.com/nasa/LSDAO

Issue Tracker

https://github.com/nasa/LSDAO/issues

Contribution Guidelines

https://github.com/nasa/LSDAO/blob/master/CONTRIBUTING.md

Ontology Download Link

https://github.com/nasa/LSDAO/blob/master/lsdao.owl

Contact Name

Dan Berrios

Contact Email

daniel.c.berrios@nasa.gov

Contact GitHub Username

DanBerrios

Contact ORCID Identifier

0000-0003-4312-9552

Formats

• OWL RDF/XML (.owl)
• OBO (.obo)
• OBO Graph JSON (.json)

Dependencies

sddo bfo ro dcterms vcard sdo dcat

Related

OBI

Usages

- user: https://nlsp.nasa.gov/
  description: NLSP uses SLSO to annotate Life Sciences Data Archive data
  examples:
    - url: 
      description: "Implementation is in progress"

Intended Use Cases and/or Related Projects

The SLSO will be used most immediately to support NASA Life Sciences Portal (https://nlsp.nasa.gov/) which hosts, among other things, the NASA Life Sciences Data Archive. Furthermore, the concepts in the SLSO are likely to be adopted into the (Beta) NASA Science Discovery Engine.

Data Sources

Many hours of interviews with NASA data archivists, program managers and other space research experts.

Additional comments or remarks

Depending on how inclusion into OBO for the SLSO goes, I will submit another request to include the nascent SDDO.

OBO Foundry Pre-registration Checklist

• I have read and understood the registration process instructions and the registration checklist.
• There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
• My term labels are in English and conform to the OBO Foundry Naming Conventions
• I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
• For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
• For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
• If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
• The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.

[pfabry]

Dear @DanBerrios,

Thank you for your submission. The review will be executed as a two stage process.

First, you will have to pass the new ontology precheck, including the OBO NOR Dashboard. Pass means that no check apart from Users and Versioning may be red.
After you have successfully passed these verfications, you will be assigned an OBO Operations committee member to review the ontology.

Usually, the review will result in an opportunity for you to improve the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This gives other members of the committee the opportunity to assess your work.

When a decision is reached by the committee you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the case at hand. Please inform us about any reasons you might have for increased urgency. You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!

[DanBerrios]

@pfabry Thank you...

[pfabry]

Your ontology has been added to the OBO NOR Dashboard and has passed the technical review. A reviewer will be assigned soon. Thank you.

[pfabry]

@DanBerrios
@zhengj2007 has been assigned to review your ontology. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

[DanBerrios]

@DanBerrios @zhengj2007 has been assigned to review your ontology. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

Great. Glad to have this check...

[zhengj2007]

I reviewed the ontology and found some issues listed as follow:

1. The ontology name and abbreviation are not consistent in the new ontology request issue tracker, new ontology GitHub site and the Isdao.owl release file.
   I think the ontology name is 'Life Sciences Data Archive Ontology' and abbreviation/prefix is 'LSDAO'.
2. Only one term 'root node' in the lsdao.owl with prefix: LSDAO. I found most of are 'LSDA'. It should be fixed and check whether all terms in LSDAO with correct prefix.
3. The ontology reused many terms from the resources other than OBO Foundry ontologies, such as (https://schema.org/, http://www.w3.org/2006/vcard/). Some of them are also available in the OBO Foundry ontologies. For example, drug (https://schema.org/Drug), Role (https://schema.org/Role), Motorcycle(https://schema.org/Motorcycle). Some have same labels with different meaning, such as Gender (http://www.w3.org/2006/vcard/ns#Gender), Female (http://www.w3.org/2006/vcard/ns#Female), Cell (http://www.w3.org/2006/vcard/ns#Cell). Is it better to relabel the terms to avoid confusion?
   Regarding reuse of existing ontology terms, I generally reused terms in other OBO Foundry ontologies. I am not sure the principle of reusing the terms other than OBO Foundry ontologies.
4. The ontology adopted some terms in OBO Foundry ontology but made some modifications and assigned the new IRI. For example, 'image' (IAO:0000101) is imported from IAO in the LSDAO ontology and also create a new term 'image' with modification and assigned ID (LSDA:0000029). If the IAO:image needs to be improved, LSDAO developers can contact IAO developers to improve the term.
5. Some terms with same labels. For example, 'image', 'document', 'dataset', etc. I remember ROBOT can check this issue. But I don't know why it does not show in the ROBOT report.

[DanBerrios]

@zhengj2007 Thanks so much for this review, Jie! Can we take each of these points in turn in commentation?

Let me ask/comment:

1. Regarding scope: We shouldn't declare the scope of this ontology as "life sciences data archive", right? That is too broad and could apply to so many other existing archives, not just NASA's Life Sciences Data Archive. That's why I thought we should declare the scope instead as "space life sciences data".... If you agree, let me know... (We started building using the ODK with the idea that "lsda" would be our desired IDSPACE -see point 2 below.) Currently on our github page, the lsdao.owl file has:

        <dcterms:description>The Space Life Sciences Ontology is an application ontology and is intended to support the operation of NASA&apos;s Life Sciences Data Archive and other systems that contain space life science research data.</dcterms:description>
 ...
        <dcterms:title>Space Life Sciences Ontology</dcterms:title>

2. IDSPACE: Thank you for pointing out the error of use of "LSDA" vs. "LSDAO"! It's weird that ODK does not complain about this... Our template tsv files use the "LSDA" prefix, but our Makefile declares "lsdao" is the "ont". I can fix our template file prefixes to match the ont.... and rebuild (i.e., "LSDAO as the prefix). Will that take care of this issue? I guess ODK doesn't require that the output file names match any particular IDSPACE prefix....

[DanBerrios]

3. We want to include the kinds of human contact concepts in vcard and to curate data sets in our archives using those concepts (things like kinds of phone numbers, parts of mailing addresses, etc.). Those concepts aren't found in existing OBO ontologies, right? Note that vcard:Cell is a cell phone number whereas OBO ontologies defining "Cell" are referring to the cells of an organism. So...the labels may collide but the meanings are drastically different. What is your suggestion in these kinds of cases? We have deliberately imported a subset of schema.org terms including Drug and Role.. We could remove those imports and any other imports which may have OBO alternatives... However, ultimately we do want our data sets curated with schema.org terms as well as OBO terms, because web crawlers (e.g., Google) look for schema.org terms and use these to display data objects in users' web browsers.... Not OBO terms/fields (right?)...

[DanBerrios]

4. "LSDAO:Image" is a special case... In NASA's LSDA, our image objects are either physical images (photographs from Apollo missions, for example) or digital files (digitized photographs), and these are both identified as instances of the same object called "image". This is probably a shortcoming of LSDA in that it doesn't distinguish between these 2 kinds of objects. That's how LSDAO:image wound up outside ICE. I think it's parent could be "continuant" but not sure ... Thoughts?

[DanBerrios]

@pfabry @zhengj2007 Are we blocked on this? Is it the lexical matching report we are waiting on? Where do I find that? Thanks...

[pfabry]

@DanBerrios I'm working on the lexical matching and will get back to you soon. Thank you.

[DanBerrios]

@DanBerrios I'm working on the lexical matching and will get back to you soon. Thank you.

OK thanks. If I need to do anything more, let me know... Note that lexical matching can occur even with vast semantic differences, as in the example I discussed above of vcard:cell (as in cell phone number) and CARO:cell...

[zhengj2007]

@DanBerrios I am on vacation now and will comment on your responses next Monday.

[DanBerrios]

@DanBerrios I am on vacation now and will comment on your responses next Monday.

Thanks, but enjoy your vacation!

[zhengj2007]

Updated manual review of LSDAO

1. Ontology scope

• The terms fall within the ontology’s stated target domain of knowledge. However, the scope of the ontology is mainly covered by OBI and IAO.

2. Terms with the new ontology prefix

• Do the terms follow the OBO identifier scheme? yes
• Are there terms with the same meaning available in another OBO Foundry ontology? yes, for example, 'strain' seems same as OBI:0001185 selectively maintained organism.
• Is there another OBO Foundry ontology whose scope covers any of the new terms? yes, most newly added classes in LSDAO are in IAO and OBI scopes, such as biospecimen, dataset, document, experiment, institution, investigator, subject, etc.
• In addition, LSDAO added some new terms that derived from existing OBO Foundry ontology terms with more specific meaning but reused label, such as IAO:dataset, IAO:image. Recommend to relabel the term.

3. Correct use of imported terms

• If the ontology reuses terms from other OBO ontologies, are they used accurately? yes
• Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment? yes
• Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense? N/A, no additional axioms added in the ontology
• 'assay' import from SDDO rather than OBI
• Some terms imported from non-OBO Foundry ontologies although they are available in OBO Foundry ontologies. For example, Drug (from https://schema.org/Drug), Gender (from http://www.w3.org/2006/vcard/ns#Gender), Address (http://www.w3.org/2006/vcard/ns#Address), Dataset (https://schema.org/Dataset).

4. Basic review of axiomatic patterns

• Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.) The axioms are simply and appropriately constructed.
• Are existential restrictions used correctly? yes for the relations defined OBO Foundry ontologies (mainly RO relations). not sure for the relations defined non-OBO Foundry ontologies/terminologies (e.g. schema.org, vcard, DCAT 2) and the new ontology request as a member of OBO Foundry ontologies (i.e. LSDAO and SDDO) since these relations are either no definitions or no specified domain/range or not used.

5. Appropriate use of object properties

• Are object properties used in a manner consistent with their definitions, domain, and range? yes for OBO Foundry ontologies. not sure for the relations defined non-OBO Foundry ontologies/terminologies (e.g. schema.org, vcard, DCAT 2) and the new ontology request as a member of OBO Foundry ontologies (i.e. LSDAO and SDDO) since these relations are either no definitions or no specified domain/range or not used.
• Too many relations are not defined in RO. Need consider to add the relations to RO when the ontology accepted by OBO Foundry.

6. Responsiveness to suggested changes: ✅ yes. As evidenced above, the ontology developer has been very responsive to requests for changes and other queries.

Additional Questions/Suggestions

1. The ontology named as "Life Sciences Data Archive Ontology" in the ontology github repository. However, it is named as 'Space Life Sciences Ontology' in the request with abbreviation "SLSO'. The request prefix is LSDAO. It's confused. May consider to use "SLSO" as identifier space.
2. The ontology reused many non-OBO Foundry ontology terms. Discussed on Feb 20, 2024 OBO operation committee meeting, it is better to reuse existing OBO Foundry ontology terms or add the terms in LSDAO and provide the mappings to those non-OBO Foundry ontology terms.
3. Although the ontology passed the OBO dashboard checking, many errors are found when I ran robot report --input lsdao.owl. It may due to wrong identifier space used in the ontology when checked. Here are some errors:

Rule Name	Subject	Property	Value
duplicate_definition	obo:LSDAO_0001111	IAO:0000115	Duty center of the NASA representative
duplicate_definition	obo:LSDAO_0001163	IAO:0000115	Duty center of the NASA representative
duplicate_label	obo:LSDAO_0000042	rdfs:label	strain
duplicate_label	obo:LSDAO_0001162	rdfs:label	strain
duplicate_label	obo:LSDAO_0000053	rdfs:label	research area
duplicate_label	obo:LSDAO_0001145	rdfs:label	research area
duplicate_label	obo:LSDAO_0001142	rdfs:label	program name
duplicate_label	obo:LSDAO_0001148	rdfs:label	program name
duplicate_label	obo:LSDAO_0001152	rdfs:label	program name
duplicate_label	obo:LSDAO_0001160	rdfs:label	program name
duplicate_label	obo:LSDAO_0000027	rdfs:label	program
duplicate_label	obo:LSDAO_0001117	rdfs:label	program
duplicate_label	obo:LSDAO_0001133	rdfs:label	principal investigator
duplicate_label	obo:LSDAO_0001136	rdfs:label	principal investigator
duplicate_label	obo:LSDAO_0001149	rdfs:label	payload ID
duplicate_label	obo:LSDAO_0001161	rdfs:label	payload ID
duplicate_label	obo:LSDAO_0000009	rdfs:label	implements
duplicate_label	obo:LSDAO_0000013	rdfs:label	implements
duplicate_label	obo:LSDAO_0000010	rdfs:label	implementedBy
duplicate_label	obo:LSDAO_0000014	rdfs:label	implementedBy
duplicate_label	obo:LSDAO_0001080	rdfs:label	description
duplicate_label	obo:LSDAO_0001168	rdfs:label	description
duplicate_label	dc:description	rdfs:label	description
duplicate_label	http://www.w3.org/ns/dcat#Dataset	rdfs:label	Dataset@en
duplicate_label	http://www.w3.org/ns/dcat#dataset	rdfs:label	dataset@en
duplicate_label	https://schema.org/Dataset	rdfs:label	Dataset@en
duplicate_label	https://schema.org/dataset	rdfs:label	dataset@en
duplicate_label	obo:LSDAO_0001096	rdfs:label	component name
duplicate_label	obo:LSDAO_0001146	rdfs:label	component name
duplicate_label	RO:0000087	rdfs:label	has role@en
duplicate_label	http://www.w3.org/2006/vcard/ns#hasRole	rdfs:label	has role@en
duplicate_label	OBI:0100026	rdfs:label	organism@en
duplicate_label	obo:SDDO_3000065	rdfs:label	organism@en

Please run robot report to obtain full list of errors.

[DanBerrios]

@zhengj2007 Thank you! I will be looking over the duplicates and other issues you mentioned above from robot report.

Regarding scope and term re-use, our plan has been to sub-class or otherwise re-use from existing OBO ontologies wherever possible. I guess we missed some of the opportunities to do that for things like OBI:strain. We have the complicating factor that our database sometimes doesn't represent things like strains as object, but instead as text metadata for other objects ("subject" has a data property "strain", instead of an object property). We will fix those and other opportunities to reuse wherever we can.

We probably also over-imported from schema.org and vcard and could pare back to only a few imported concepts from those... this will also reduce concept label duplication.

[DanBerrios]

@zhengj2007 And do let me know if you and the Committee feel strongly that we should change our prefix space to something like SLSO from LSDAO. It would be quite a bit of work to do it, but possible...

[zhengj2007]

@zhengj2007 And do let me know if you and the Committee feel strongly that we should change our prefix space to something like SLSO from LSDAO. It would be quite a bit of work to do it, but possible...

@DanBerrios I will raise it on tomorrow's meeting and let you know the Committee's decision.

[zhengj2007]

@DanBerrios Discussed on 2024-03-05 OBO operation committee meeting. It recommended that you use the ID space SLSO for the ontology.

[DanBerrios]

@zhengj2007 LOL it's recommended by myself also. I just fear the work to make the change...not sure of all the hooks using ODK that I will need to change, but I will have a go at it in a branch today.

[DanBerrios]

@zhengj2007 OK, I've made the IDSPACE update and other actions responsive to ROBOT report (but still in work on lots of those). Here's a draft release of the "SLSO": https://github.com/nasa/LSDAO/releases/tag/v2024-03-05
Our archivists are going to review the changes with me this week and then we can merge it into master branch.

[zhengj2007]

@DanBerrios Great! Please let me know when the ontology is ready for me to review again.

[pfabry]

At last! Thanks to @cthoyt, below are the positive results of the lexical match. All results are in the enclosed file. LSDAO lexmatch 20240312.txt

Lexical matching returned results

• LSDA:0000009 implements
  • swo:0000740 implements (0.778)
• LSDA:0000013 implements
  • swo:0000740 implements (0.778)
• LSDA:0000016 owns
  • obib:0000732 owns (0.778)
• LSDA:0000021 dataset
  • mi:0875 dataset (0.778)
  • t4fs:0000347 dataset (0.778)
• LSDA:0000022 experiment
  • agro:00000369 experiment (0.778)
  • proco:0000014 experiment (0.778)
• LSDA:0000024 investigator
  • opmi:0000293 investigator (0.778)
  • tto:102017 Nemichthys (0.54)
  • vto:0034242 Nemichthys (0.54)
• LSDA:0000028 document
  • iao:0000310 document (0.778)
• LSDA:0000029 image
  • iao:0000101 image (0.778)
  • chebi:147370 imazaquin-ammonium (0.54)
• LSDA:0000032 spacecraft
  • envo:01003000 spacecraft (0.778)
  • rbo:00000033 spacecraft (0.778)
• LSDA:0000036 component
  • mi:0354 cellular component (0.556)
• LSDA:0000042 strain
  • aro:3004531 strain (0.778)
  • iceo:0000065 strain (0.778)
  • ncbitaxon:strain strain (0.778)
  • pato:0001034 strain (0.778)
  • xco:0001265 stress (0.556)
• LSDA:0000043 scientific name
  • nomen:0000036 scientific name (0.778)
• LSDA:0000045 role
  • bfo:0000023 role (0.778)
  • chebi:50906 role (0.778)
  • uberon:2002175 rostral octaval nerve motor nucleus (0.54)
  • zfa:0001698 rostral octaval nerve motor nucleus (0.54)
• LSDA:0000047 institution
• LSDA:0001056 release date
  • ms:1001017 release date (0.778)
• LSDA:0001058 duration
  • apollosv:00000243 duration (0.778)
  • exo:0000054 duration (0.778)
  • pato:0001309 duration (0.778)
  • sbo:0000347 duration (0.778)
• LSDA:0001067 document title
  • iao:0000305 document title (0.778)
• LSDA:0001080 description
  • apollosv:00000476 description (0.778)
• LSDA:0001082 fixative
  • chebi:50913 fixative (0.778)
• LSDA:0001083 age
  • exo:0000102 age (0.778)
  • fbdv:00007013 age (0.778)
  • pato:0000011 age (0.778)
  • wbphenotype:0000039 life span phenotype (0.54)
  • wbphenotype:0000061 extended life span (0.54)
  • wbphenotype:0001171 shortened life span (0.54)
  • chebi:84123 advanced glycation end-product (0.484)
• LSDA:0001086 gender
  • gecko:0000060 gender (0.778)
  • nomen:0000045 gender (0.778)
  • exo:0000110 sex (0.556)
• LSDA:0001098 hardware type
  • ontoavida:00000141 hardware type (0.778)
• LSDA:0001099 city
  • envo:00000856 city (0.778)
• LSDA:0001116 measurements
  • exo:0000067 measurement (0.778)
• LSDA:0001122 data source
  • mi:1053 data source (0.778)
  • ohd:0000053 data source (0.778)
• LSDA:0001124 Creator
  • ncbitaxon:2926223 Creator (0.778)
• LSDA:0001125 project name
• LSDA:0001126 location
  • exo:0000017 location (0.778)
  • pato:0000140 position (0.556)
  • pato:0000605 obsolete placement value (0.556)
• LSDA:0001133 principal investigator
  • agro:00000380 principal investigator (0.778)
  • opmi:0000411 principal investigator (0.778)
  • t4fs:0000441 principal investigator (0.778)
• LSDA:0001134 investigators
  • opmi:0000293 investigator (0.778)
• LSDA:0001136 principal investigator
  • agro:00000380 principal investigator (0.778)
  • opmi:0000411 principal investigator (0.778)
  • t4fs:0000441 principal investigator (0.778)
• LSDA:0001139 agency
  • gsso:010894 agency (0.778)
• LSDA:0001140 discipline
  • gsso:001304 discipline (0.778)
• LSDA:0001143 species
  • apollosv:00000121 species (0.778)
  • ncbitaxon:species species (0.778)
  • nomen:0001020 species (0.778)
  • taxrank:0000006 species (0.778)
  • tto:species species (0.778)
• LSDA:0001151 investigators
  • opmi:0000293 investigator (0.778)
  • tto:102017 Nemichthys (0.54)
  • vto:0034242 Nemichthys (0.54)
• LSDA:0001158 Year
  • opmi:0000353 year (0.762)
  • uo:0000036 year (0.762)
  • ogg:3000946317 yeaR (0.744)
• LSDA:0001162 strain
  • aro:3004531 strain (0.778)
  • iceo:0000065 strain (0.778)
  • ncbitaxon:strain strain (0.778)
  • pato:0001034 strain (0.778)
  • xco:0001265 stress (0.556)
• LSDA:0001163 center
  • poro:0000188 spicule center (0.556)
• LSDA:0001168 description
  • apollosv:00000476 description (0.778)
• LSDA:0001169 weight
  • pato:0000128 weight (0.778)
• LSDA:0001172 genotype
  • exo:0000107 genotype (0.778)
  • geno:0000536 genotype (0.778)
  • mco:0000383 genotype (0.778)
  • ncbitaxon:genotype genotype (0.778)
  • so:0001027 genotype (0.778)

[DanBerrios]

@pfabry Thanks for this report! This will help us improve the SLSO. We are meeting this week to continue to address the duplicate label/concept issues... Question: the bioregistry.io links in the above above report don't resolve when I tried them... I resorted to looking up some on Bioportal (Ontobee also has been having trouble lately)...do we expect the OLS/Bioregistry links to start working soon?

[cthoyt]

hmm, it appears there are a few CURIES that aren't quite making sense like ncbitaxon:genotype. Bioregistry is normally just passing through to other services, so there might be an issue at the moment with the OBO PURL system, OLS or OntoBee. https://bioregistry.io/ seems to be up at the moment

[DanBerrios]

@cthoyt @pfabry Yeah the main bioregistry site does appear up, but the curie/OBO ID search doesn't seem to be working... if it's relying on Ontobee calls, that could be the reason why. For Taxon and other ontologies in Bioportal, I can see those concepts there.... just takes an extra step though. Hopefully Ontobee issues will be sorted out soon...

[DanBerrios]

@cthoyt @pfabry @zhengj2007 So..there are some oddities with this report on lexical label matching... For example:

• LSDA:0000024 investigator
  • tto:102017 Nemichthys (0.54)

?? not sure how I see there's any lexical matching between "investigator" and that taxon...

And similar weird lexical label matching for SLSO:role, SLSO:image, etc....

[DanBerrios]

@zhengj2007 Thanks for your patience! We worked hard to shape up the SLSO. The duplicated label and other ODK reports helped a lot. We removed a lot of duplicated properties and fixed a few blatant errors. We still have some more work to do even after addressing those issues. However, I think it's in a place that you can check it out again. I put all the changes in this release: [https://github.com/nasa/LSDAO/releases/tag/v2024-03-26] for you to check out. (This release was built from the berrios032224 branch in GitHub).

We fixed many cases where we had labels colliding with other OBO ontology objects. A lot of the remaining cases where our objects still collide with other OBO object labels aredue to those other ontologies:

1. Using a different object type (class vs. data property, for example) from what we chose to use
2. Defining objects that are not limited to the scope of their ontologies
3. Defining object that overly specified in their definitions despite very broad labels.

We did the best we could for now in trying to minimize these. Let me know your thoughts....

[zhengj2007]

@DanBerrios Thanks for the updates. I will review SLSO again before next operation meeting.

I have one question. The ontology is named as Space life Sciences Ontology with SLSO prefix. Will the SLSO ontology keep the repository name LSDAO? I found the LSDAO repository readme contains following header and description:
"Life Sciences Data Archive Ontology
Description: The Life Sciences Data Ontology is an application ontology and supports the operation of NASA's Life Sciences Data Archive"
Besides, the request prefix in the tracker haven't changed to SLSO yet.

[DanBerrios]

If GH let's me change the repo name, I can/will.... I haven't merged the branch with this work into master yet, but when I do, the repo should get the updated name and description in the README.md.... I was waiting on your review to do the merge....
I updated the requested prefix now in this issue... @zhengj2007

[zhengj2007]

@DanBerrios I downloaded the slso from the link you provided. The slso.owl with version IRI:
http://purl.obolibrary.org/obo/slso/releases/2024-03-26/slso.owl.

I ran the robot command: robot report --input slso.owl --output report.tsv and got 444 errors. Although most of errors caused by labels and definitions of terms in different languages, there are some errors need to be fixed:

• used deprecated terms, e.g. OMRSE:00000020
• SLSO_0001162 has same definition as OBI:0001185
• same label used for more than one term, e.g. 'specimen' for OBI:0100051 and obo:SDDO_3000078
• some imported terms with multiple labels and different from those in source ontology, such as GO:0003674 with label 'gene product or complex activity' and 'molecular_function'

Besides, SLSO reused many non-OBO vocabularies/terminologies. Might consider to provide the term mappings of non-OBO vocabularies/terminologies to OBO ontologies if possible.

[zhengj2007]

@DanBerrios Discussed on 2024-04-02 OBO operation committee. The ontology has been tentatively accepted. Once the SLSO passed the OBO dashboard, it can move to the next step. You may contact @pfabry to replace LSDAO with SLSO in the dashboard.

[DanBerrios]

@zhengj2007 Thanks! Did you want me to merge the SLSO rename into my master branch on GH now? @pfabry Let me know what I need to do next....

[zhengj2007]

Thank you again for your ontology submission to the OBO Foundry. We are happy to inform you that your ontology (SLSO) has been accepted following discussion in the OBO Operations Committee meeting, 2024-04-02. Before we can add it to the OBO ontology registry you need to complete the following steps:

Create a metadata record for your ontology to be included in the registry:

Create a new file in https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology, called YOURID.md (there is an “Add file” button in the top right).
Obtain the already curated metadata that relates to your ontology from https://github.com/OBOFoundry/obo-nor.github.io/blob/master/dashboard-config.yml (you'll need to scroll down to locate yours; it will have your prefix in the " - id:" field.)
Create a pull request to add the metadata record. This pull request should include a link to this issue (the New Ontology Request issue).
Here is an example record for the PATO ontology: https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/pato.md?plain=1

Your metadata will be reviewed and merged by a member of the OBO Foundry Operations Committee. Permissible content for fields is being documented here.

To create a PURL registry entry for your ontology:

Go to https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config, click “Add file” and add a file named YOURID.yml.
Add the desired configuration.
Make a pull request with a link to this issue See here for an example of a PURL yml file: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/pato.yml

[zhengj2007]

@DanBerrios Please see the instructions I posted.

[DanBerrios]

@zhengj2007 Thanks! It's in work...

[nicolevasilevsky]

This is online and can be closed. Thanks so much!