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New Ontology Request: NGBO #1819

Closed Dalalghamdi closed 1 year ago

Dalalghamdi commented 2 years ago

Ontology title

Next Generation Biobanking Ontology

Requested ID space

NGBO

Ontology location

https://github.com/Dalalghamdi/NGBO

Contact person

Name:Dalia Alghamdi Email address: dal.alghamdi92@gmail.com GitHub username: dalalghamdi

Issue tracker

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

Version Controlled Repository

Ontology license

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.

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: dal.alghamdi92@gmail.com
  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 commented 2 years ago

@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 commented 2 years ago

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.

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 commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@matentzn Thank you, I updated my request.

matentzn commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

I will have to run it unfortunately!

matentzn commented 2 years ago

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

Dalalghamdi commented 2 years ago

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

matentzn commented 2 years ago

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

Dalalghamdi commented 2 years ago

@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: dal.alghamdi92@gmail.com
 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 commented 2 years ago

What is your orcid?

matentzn commented 2 years ago
Dalalghamdi commented 2 years ago

all fixed

matentzn commented 2 years ago
Dalalghamdi commented 2 years ago

my orcid is 0000-0002-2801-0767

matentzn commented 2 years ago

@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 image
  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 commented 1 year ago

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

matentzn commented 1 year ago

Hey @Dalalghamdi not all errors are fixed yet!

Dalalghamdi commented 1 year ago

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 commented 1 year ago

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

Also, You have whitespace around the title!

matentzn commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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?

2022-10-05
Dalalghamdi commented 1 year ago

Thank you @matentzn

matentzn commented 1 year ago

@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!

matentzn commented 1 year ago

Actually there is already a reviewer assigned: @bpeters42 NGBO is now ready for review.

bpeters42 commented 1 year ago

I looked through the file, and found a large number of problems everywhere I looked:

But as I understand these terms are defined outside of NGBO, and reflect problems at large. It is unclear / hard for me to review what specifically NGBO is doing.

bpeters42 commented 1 year ago

This was discussed in the OBO operations call on 10/18, but discussion was cut short because we ran out of time. Current status was:

I hope I captured all, but most of all I wanted to say that the overall feedback is positive, and we very much appreciate the work put into making the technical requirements pass.

Dalalghamdi commented 1 year ago

@bpeters42 Thank you so much for your feedback, I appreciate your time and effort.

  • strong encouragement to submit all NGBO terms to reference ontologies (OBI, etc), but understanding that NGBO is needed as an application ontology now, and can't wait for term requests. Positive feedback that this is already happening (thank you!)

Great, I am still committed to submitting most of the NGBO terms to reference ontologies, mainly OBI and SWO. I prepared ROBOT sheets for the submission, but they still need a lot of work and revision as I have done a lot of changes. Hopefully will get this done sometime in the new year. However, I think I will still need to use NGBO even if the terms existed elsewhere. I have a couple of use cases where I am using ontology features to test; (i)Specimen tracking and traceability (ii) Data privacy and user access control in a federated query tool . I think the modeling might be out of reference ontologies scope for now.

  • issues pointed out in my last comment are not the fault of NGBO, but reflect the difficulty of importing terms from multiple ontologies with little guidance. Recommendation to switch to the COB, which gives a higher base to import terms in; recommendation to stick to primary identifiers from OBO ontologies for imported terms (and not e.g. EFO), and to add annotations if imports are recognized as problematic.

I had a look at COB, and I agree; I will plan to switch soon. Also, I will revisit all imported terms. I tried to avoid re-inventing the wheels, but I agree that should have considered other important things; thank you for pointing this out.

  • vote on acceptance or not will be done in next meeting

please let me know If there is anything I can do to get NGBO accepted; thank you again!

bpeters42 commented 1 year ago

Thank you again for your ontology submission to the OBO Foundry. We are happy to inform you that your ontology (NGBO) has been accepted following discussion in the OBO Operations Committee meeting, 2022-11-29. 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

deepakunni3 commented 1 year ago

NGBO has been added to the OBOFoundry metadata via #2214

@Dalalghamdi - OLS will automatically pick up new OBO ontologies. However, there is a lot of work on the infrastructure at the moment there, and it may be worth to ask them if NGBO does not appear in OLS by the end of January.