Closed DanBerrios closed 3 months ago
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!
@pfabry Thank you...
Your ontology has been added to the OBO NOR Dashboard and has passed the technical review. A reviewer will be assigned soon. Thank you.
@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 @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...
I reviewed the ontology and found some issues listed as follow:
@zhengj2007 Thanks so much for this review, Jie! Can we take each of these points in turn in commentation?
Let me ask/comment:
<dcterms: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.</dcterms:description>
...
<dcterms:title>Space Life Sciences Ontology</dcterms:title>
@pfabry @zhengj2007 Are we blocked on this? Is it the lexical matching report we are waiting on? Where do I find that? Thanks...
@DanBerrios I'm working on the lexical matching and will get back to you soon. Thank you.
@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...
@DanBerrios I am on vacation now and will comment on your responses next Monday.
@DanBerrios I am on vacation now and will comment on your responses next Monday.
Thanks, but enjoy your vacation!
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.
@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.
@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 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.
@DanBerrios Discussed on 2024-03-05 OBO operation committee meeting. It recommended that you use the ID space SLSO for the ontology.
@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.
@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.
@DanBerrios Great! Please let me know when the ontology is ready for me to review again.
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
@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?
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
@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...
@cthoyt @pfabry @zhengj2007 So..there are some oddities with this report on lexical label matching... For example:
?? 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....
@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:
We did the best we could for now in trying to minimize these. Let me know your thoughts....
@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.
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
@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:
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.
@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.
@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....
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
@DanBerrios Please see the instructions I posted.
@zhengj2007 Thanks! It's in work...
This is online and can be closed. Thanks so much!
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
Dependencies
sddo bfo ro dcterms vcard sdo dcat
Related
OBI
Usages
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
dc:license
annotation, serialised in RDF/XML.