New Ontology Request: NGBO

[Dalalghamdi]

Ontology title

Next Generation Biobanking Ontology

Requested ID space

NGBO

Ontology location

https://github.com/Dalalghamdi/NGBO

Contact person

Name:Dalia Alghamdi Email address: [email protected] GitHub username: dalalghamdi

Issue tracker

https://github.com/Dalalghamdi/NGBO/issues

Version Controlled Repository

Ontology license

• [ Yes ] CC0 (public domain)
• [ ] CC-BY (version 3 or later)
• [ ] Other: please specify

Available ontology formats

OWL-RDF/XML - OBO foundry format

What domain is the ontology intended to cover?

Biobank data repositories

Related OBO Foundry ontologies

OBIB - OBI

Intended use/related projects

To build a federated query platform for the Saudi Human Genome Project (SHGP). SHGP is a genetic database for the Saudi population; the project collects data sets from seven different sites. In this project, we demonstrate how semantic web technologies (e.g., SPARQL, RDF, ontologies) can be used to build an application that aims to improve querying and integrating biobank specimens and specimen-derivative data such as genomic sequences. We set up a web application for end-users with appropriate functions to import, query, and retrieve the data using the SPARQL API and queries against RDF triples stored in a graph database. The semantic web application is freely available and licensed under the Apache License 2.0 at: https://github.com/Dalalghamdi/NGBOProject.

The ontology also covers College of American Pathologists (CAP) reporting and documentation requirements to collect contextual data relevant to any given experiment's primary analysis. This is intended for the unplanned secondary use of the data for further research that might require additional contextual data. Thus, all seven sites will document and report required data items.

The ontology is maintained in GitHub, and improvement will continue based on community input and feedback from users; also, Since NGBO is an application ontology, NGBO-defined terms will be submitted to relevant domain ontologies. In our future work, we will continue the data curation efforts by completing the metadata management proposal for the Saudi Human Genome Project

Data source

Saudi Human Genome Project (User interview) King Fahad Medical City (User interview) College of American Pathologists (CAP) Other genomics metadata reporting requirements

Additional comments or remarks

NGBO is an application ontology, new terms introduced by NGBO will submitted to the appropriate OBO foundry domain ontology when possible.

OBO Foundry pre-registration checklist

To be considered for inclusion in the OBO Foundry, an ontology must meet certain requirements, as described in in the registration process instructions and the registration review checklist. To ensure you are aware of some of its key points, please review the checklist below.

You can either check a box by submitted the request first and then using the GitHub interface, or replacing the - [ ] by - [X] in the following.

• [X] I have read and understood the registration process instructions and the registration checklist
• [x] There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there was, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• [X] My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• [X] I understand that term definitions, while not mandatory, 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 have definitions, using the IAO:0000115 property.
• [X] 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).
• [X] For all relationship properties (Object and Data Property) I checked whether RO includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• [X] 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.
• [x] 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.
• [X] The requested ID space does not conflict with another ID space found in other registries such as BioPortal and the Bioregistry, see here for a complete list.

Metadata

Please fill in the following metadata record which will be used by the OBO Foundry website. Note that the values shown are just examples, for example yourfourletterid could be something like aism, cohm, mondo (it does not have to be four letters). your_domain_like_for_example_anatomy could be simply anatomy, and the license should be whatever your actual license is. An example can be found here, but you really only need to fill in the metadata mentioned here.

id: Igbo
title: Next generation biobanking ontology
contact:
  email: [email protected]
  label: Dalia Alghamdi
description: 
The ontology focuses on capturing the information about three main omics data generation activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.

domain: biobanking ontology
homepage: https://github.com/Dalalghamdi/NGBO
products:
  - id: ngbo.owl
  - id: ngbo.obo
dependencies:
  - id: ro
tracker: https://github.com/Dalalghamdi/NGBO/issues
license:
  url: http://creativecommons.org/licenses/by/3.0/
  label: CC-BY
usages:

[matentzn]

@Dalalghamdi Thank you for your submission! We will start looking at your request as soon as all the checkboxes above are checked. Let us know if you need any help!

[bpeters42]

Just looking at the textual description, this seems to overlap completely with the scope of OBI, and I don't believe any contact has been made.

• Bjoern

On Thu, Mar 31, 2022 at 5:29 AM Nico Matentzoglu @.***> wrote:

@Dalalghamdi https://github.com/Dalalghamdi Thank you for your submission! We will start looking at your request as soon as all the checkboxes above are checked. Let us know if you need any help!

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1819#issuecomment-1084516737, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2ISVX4YO2WX4B2NFAKTVCWLBHANCNFSM5RZ4E4EQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[DanBerrios]

@bpeters42 This submission says it is for an application ontology... Isn't OBI a domain ontology? If so, wouldn't overlap be a non-issue?

[bpeters42]

@DanBerrios , It is not completely clear to me if this is indeed an application ontology, and what the driving application is. Dalia has now contacted OBI by email, and we are having that discussion there, which I am sure you have seen. Just putting this note here so that others can see that we didn't simply drop this.

[Dalalghamdi]

@matentzn Thank you, I updated my request.

[matentzn]

@Dalalghamdi I looked at your repo and cannot find the release ngbo.owl version, only the editors file. Can you please create a release version and provide a link here?

[Dalalghamdi]

@Dalalghamdi I looked at your repo and cannot find the release ngbo.owl version, only the editors file. Can you please create a release version and provide a link here?

Thank you @matentzn, here you go https://github.com/Dalalghamdi/NGBO/blob/master/src/ontology/ngbo.owl

[matentzn]

Before we can start reviewing your ontology, you have to pass minimum QC thresholds:

https://obofoundry.org/obo-nor.github.io/dashboard/ngbo/dashboard.html

Let us know if you need help fixing these errors. You don't have to fix usages.

[Dalalghamdi]

@matentzn I fixed all errors. I am wondering if it's possible to run the QC myself just to check that all requirements are met?

[matentzn]

I will have to run it unfortunately!

[matentzn]

Hm, I still see many errors: https://obofoundry.org/obo-nor.github.io/dashboard/ngbo/dashboard.html

[Dalalghamdi]

Dear @matentzn, apologies for the delay. Hopefully, all errors should be fixed now. Thank you

[matentzn]

@Dalalghamdi I have updated the report! Seems like there are still issues!

[Dalalghamdi]

@matentzn OK! I admit that I'm not sure how to fix the errors. I followed the review criteria and added the sections accordingly. I pasted my ngbo.md file content below. Would you kindly let me know what I'm doing wrong? The missing definitions are added. Also dc:license and owl:versioninfo is added to the ontology owl files. Your support is appreciated Nico, many thanks.

---
layout: ontology_detail
id: ngbo
title: next generation biobanking ontology
jobs:
  - id: https://travis-ci.org/Dalalghamdi/next-generation-biobanking-ontology
    type: travis-ci
build:
  checkout: git clone https://github.com/Dalalghamdi/next-generation-biobanking-ontology.git
  system: git
  path: "."

description: next generation biobanking ontology is an open application ontology
representing omics contextual data

domain: stuff
homepage: https://github.com/Dalalghamdi/next-generation-biobanking-ontology
products:
  - id: ngbo.owl
  - id: ngbo.obo
contact:
 email: [email protected]
 label: Dalia Alghamdi
 github: dalalghamdi
dependencies:
 - id: ro
 - id: bfo
tracker: https://github.com/Dalalghamdi/next-generation-biobanking-ontology/issues
license:
  url: http://creativecommons.org/licenses/by/4.0/
=======
license: http://creativecommons.org/licenses/by/4.0/
  url: http://creativecommons.org/licenses/by/4.0/
  label: CC-BY
  usages:
- user: https://shgp.kacst.edu.sa/index.en.html
  description: Saudi Human Genome Program
  examples:
   - url: https://github.com/Dalalghamdi/NGBOSemanticWebApplication
     description: an ontology-based
web application for end-users with appropriate functions to discover and request the
specimen-derived data from SPARQL endpoints using a data federation approach

data-version: 2022-06-14
---

Enter a detailed description of your ontology here

[matentzn]

What is your orcid?

[matentzn]

• <dc:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> you should use dc terms, not dc elements for the license.
• you need to provide a valid orcid in your contact details
• you have to provide a valid version IRI like: <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/obi/2014-12-03/obi.owl"/>. User ROBOT to set this dynamically: https://robot.obolibrary.org/annotate

[Dalalghamdi]

• <dc:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/> you should use dc terms, not dc elements for the license.
• you need to provide a valid orcid in your contact details
• you have to provide a valid version IRI like: <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/obi/2014-12-03/obi.owl"/>. User ROBOT to set this dynamically: https://robot.obolibrary.org/annotate

all fixed

[matentzn]

• [ ] The Ontology IRI is not the same as the version IRI:

  <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ngbo/2020-08-01/ngbo.owl">
          <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ngbo/2020-08-01/ngbo.owl"/>
  

  should be:

  <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ngbo.owl">
          <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ngbo/2020-08-01/ngbo.owl"/>
  

• [ ] What is your orcid? - You should share it here!

• [ ] xmlns:terms="http://purl.org/dc/terms/1.1/ is the wrong namespace

[Dalalghamdi]

my orcid is 0000-0002-2801-0767

[matentzn]

@Dalalghamdi I have now implemented a way for you to manage your own metadata. Basically what you need to do:

1. Go to: https://github.com/OBOFoundry/obo-nor.github.io/blob/master/dashboard-config.yml
2. Edit the file by clicking on the pencil
3. Make changes to your ngbo related metadata.
4. Click "propose changes" and make a pull request.

Try to add your orcid (look at the other ontologies in the file to on how to do that) and make any other necessary changes.

Let me know how it goes.

[Dalalghamdi]

@matentzn Hi Nico, is there any updates regarding this request?

[matentzn]

Hey @Dalalghamdi not all errors are fixed yet!

[Dalalghamdi]

Hi @matentzn,

so for the missing Open, missing_ontology_description, and missing_ontology_title; I fixed the following (OWL files)

    <dcterms:description>The Next Generation Biobanking Ontology (NGBO) is an open-source ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.</dcterms:description>
    <dcterms:license> "http://creativecommons.org/licenses/by/4.0/" </dcterms:license>
    <dcterms:title> Next generation biobanking ontology (NGBO) </dcterms:title>

For the Plurality of Users, I edited the dashboard-config.yml , I belive you can see my commit

I hope this solve the errors

[matentzn]

Check here for correct formatting: https://oboacademy.github.io/obook/reference/formatting-license/ (especially licence)

Also, You have whitespace around the title!

[matentzn]

For the Plurality of Users, I edited the dashboard-config.yml , I belive you can see my commit

I cannot! You will have yo make a pull request for me to see it!

[Dalalghamdi]

Check here for correct formatting: https://oboacademy.github.io/obook/reference/formatting-license/ (especially licence)

Also, You have whitespace around the title!

My apologies @matentzn for taking this long, I appreciate your time and effort. It should be fine now I fixed it as instructed

<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ngbo.owl">
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string"> Next Generation Biobanking Ontology (NGBO) is an open application ontology representing contextual data about omics digital assets in biobank. The ontology focuses on capturing the information about three main activities: wet bench analysis used to generate omics data, bioinformatics analysis used to analyze and interpret data, and data management.</dc:description>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string"> Next generation biobanking ontology(NGBO).</dc:title>
    <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/" />
    <owl:versionInfo>2022-10-05</owl:versionInfo>
</owl:Ontology>

[matentzn]

almost - seems only one error remaining: https://obofoundry.org/obo-nor.github.io/dashboard/ngbo/dashboard.html

http://creativecommons.org/licenses/by/4.0/

should be

https://creativecommons.org/licenses/by/4.0/

(note the s)

You need to update the ontology and the metadata!

[Dalalghamdi]

almost - seems only one error remaining: https://obofoundry.org/obo-nor.github.io/dashboard/ngbo/dashboard.html

http://creativecommons.org/licenses/by/4.0/

should be

https://creativecommons.org/licenses/by/4.0/

(note the s)

You need to update the ontology and the metadata!

is the following correct for versioning IRI? <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-10-05</owl:versionInfo> <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ngbo/2022-10-05/ngbo.owl"/>

[Dalalghamdi]

Thank you @matentzn

[matentzn]

@Dalalghamdi thank you - the ontology is now ready for review by the OBO Operations review committee. They will elect a reviewer in the coming weeks who will review the contents of your ontology. Please remember that regardless of the outcome of the review, you have done a great job already improving the FAIRness of your ontology!