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TOXic Process Ontology (TXPO) #1057

Closed txpo-ontology closed 4 years ago

txpo-ontology commented 4 years ago

Ontology title

Toxic Process Ontology

Requested ID space

TXPO

Ontology location

Home page: https://toxpilot.nibiohn.go.jp Github: https://github.com/txpo-ontology/TXPO

Contact person

Name: Yuki Yamagata Email address: y-yamagata@nibiohn.go.jp GitHub username: txpo-ontology

Issue tracker

https://github.com/txpo-ontology/TXPO/issues

Ontology license

Available ontology formats

OWL

What domain is the ontology intended to cover?

TOXic Process Ontology (TXPO) systematizes a wide variety of terms involving toxicity courses and processes. The first version of TXPO focuses on liver toxicity.

Related OBO Foundry ontologies

BFO, GO, UBERON, CL (Cell Ontology), ChEBI, PATO, DOID, Relational ontology (RO)

Intended use/related projects

Knowledge systematization for toxic processes for drug safety evaluation

Data source

From textbooks ,we researched drug-induced hepatotoxic mechanisms and obtained information about toxic courses and related processes, molecules and their roles, and biological structures. Next, we searched for the latest information from toxic course-related articles using PubMed.

Additional comments or remarks

Elucidating the mechanism of toxicity is crucial in drug safety evaluations. We focus on toxic processes and developed a toxic process ontology, designated TXPO. The TXPO contains an is-a hierarchy that is organized into three layers: the top layer contains general terms, mostly derived from the Basic Formal Ontology. The intermediate layer contains biomedical terms in OBO foundry, and the lower layer contains toxicological terms. More details: https://www.researchgate.net/publication/335060857

//////// Dear OBO-Discuss, We have developed the TOXic Process Ontology (TXPO), and we requested a prefix and PURL in OBO two month ago via OBO-discuss mailing list. It's been more than two months, but I haven't received the response yet. So, I’ll send the request again just in case.

Sincerly, Yuki Yamagata, Ph.D.

ramonawalls commented 4 years ago

The request for an OBO Foundry PURL was approved today at the Operations Committee meeting. There were some concerns about overlap with other OBO ontologies, although we were encouraged to see the reuse of many terms from OBI, PATO, etc. Please feel free to reach out on the obo-discuss list or to individual ontologies if you need further coordination with existing OBO Foundry ontologies.

To activate the purl, please create a pull with the appropriate YAML files in https://github.com/OBOFoundry/purl.obolibrary.org. If you need any guidance on how to do that, let us know.

cmungall commented 4 years ago

I notice you have have many similar terms to GO under the role hierarchy. These are only linked to GO in the comments, not computationally. Is it not possible for you to use GO terms directly and request new terms where required?

txpo-ontology commented 4 years ago

I notice you have have many similar terms to GO under the role hierarchy. These are only linked to GO in the comments, not computationally. Is it not possible for you to use GO terms directly and request new terms where required?

Thank you for your comment. Yes, there are some roles in TXPO, which have the comment "related molecular function GO: XXXX.” Role is a specifically dependent continuant, and GO's molecular function is a process as occurrent. Therefore, if the process (molecular function) involved is in the GO term, I write it in the comment. But, maybe I should move them from the comment to the Database cross-reference.

Use case example of choline transmembrane transporter inTXPO. In the phospholipidosis (toxic course), "increasing glycerophospholipid material (process)” has participant “SLC44A2 (human) (molecule)”. SLC44A2 (human) has role "choline transmembrane transporter (role)”.

txpo-ontology commented 4 years ago

We created the YAML file and have successfully registered OBO Foundry. Thank you!

Yuki

pbuttigieg commented 4 years ago

@txpo-ontology

On behalf or the OBO Operations Committee, I apologise for the long waiting period in processing your request:

As new requests have come in, it became clear that a revision of our policies for inclusion of new ontologies was needed. The current state of those policies is viewable here: http://obofoundry.org/docs/Policy_for_OBO_namespace_and_associated_PURL_requests.html

If you are still interested in pursuing a prefix and IRI handling service for your submission through OBO Services, please respond to this message within two weeks (when our next OBO Operations call will take place).

If we do not hear from you, we will close this issue; however, you can always reopen it if desired. Thank you and our apologies once again.

txpo-ontology commented 4 years ago

Dear Dr. Pier Luigi But­ti­gieg,

Thank you for contacting us. Our request was already approved. TXPO on OBO-Foundry site: http://www.obofoundry.org/ontology/txpo.html

So, please close this issue. Thank you.

Kind regards,

Yuki Yamagata, Ph.D. y-yamagata@nibiohn.go.jp Laboratory of Toxicogenomics Informatics National Institutes of Biomedical Innovation, Health and Nutrition 7-6-8 Asagi, Saito, Ibaraki, 567-0085, Osaka, Japan

https://toxpilot.nibiohn.go.jp

差出人: Ramona Walls notifications@github.com 件名: Re: [OBOFoundry/OBOFoundry.github.io] TOXic Process Ontology (TXPO) (#1057) 日付: 2019年9月25日 1:38:22 JST 宛先: "OBOFoundry/OBOFoundry.github.io" OBOFoundry.github.io@noreply.github.com CC: txpo-ontology y-yamagata@nibiohn.go.jp, Author author@noreply.github.com 返信先: "OBOFoundry/OBOFoundry.github.io" reply@reply.github.com

The request for an OBO Foundry PURL was approved today at the Operations Committee meeting. There were some concerns about overlap with other OBO ontologies, although we were encouraged to see the reuse of many terms from OBI, PATO, etc. Please feel free to reach out on the obo-discuss list or to individual ontologies if you need further coordination with existing OBO Foundry ontologies.

To activate the purl, please create a pull with the appropriate YAML files in https://github.com/OBOFoundry/purl.obolibrary.org https://github.com/OBOFoundry/purl.obolibrary.org. If you need any guidance on how to do that, let us know.

—

2020/02/26 3:19、Pier Luigi Buttigieg notifications@github.com のメール：

@txpo-ontology https://github.com/txpo-ontology On behalf or the OBO Operations Committee, I apologise for the long waiting period in processing your request:

As new requests have come in, it became clear that a revision of our policies for inclusion of new ontologies was needed. The current state of those policies is viewable here: http://obofoundry.org/docs/Policy_for_OBO_namespace_and_associated_PURL_requests.html http://obofoundry.org/docs/Policy_for_OBO_namespace_and_associated_PURL_requests.html If you are still interested in pursuing a prefix and IRI handling service for your submission through OBO Services, please respond to this message within two weeks (when our next OBO Operations call will take place).

If we do not hear from you, we will close this issue; however, you can always reopen it if desired. Thank you and our apologies once again.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1057?email_source=notifications&email_token=AMF5NSYUQ6HHEJSXAKW3GNLREVOLHA5CNFSM4I2BJIK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM45XPY#issuecomment-590994367, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMF5NS4L5N6RY2XXTUXUWS3REVOLHANCNFSM4I2BJIKQ.

pbuttigieg commented 4 years ago

@txpo-ontology many thanks for your feedback Yamagata-san, closing now....