PMO prefix and PURL request

[kang-hongyu]

Requested Prefix: PMO

Ontology Title: The Precision Medicine Ontology

Download link: https://raw.githubusercontent.com/PMOntology/The-Precision-Medicine-Ontology/master/PMO_obo_sub_v2.owl

Home page: https://github.com/PMOntology/The-Precision-Medicine-Ontology

Contact e-mail: kang.hongyu@imicams.ac.cn / kanghongyu1988@163.com

Tracker link: https://github.com/PMOntology/The-Precision-Medicine-Ontology/issues

Description: PMO is an extensible ontology aimed to integrate the terms in field of precision medicine, and all of the terms and relationships in PMO can apply in text mining or knowledge base building. PMO supports the identification and semantic integration of gene, disease, drug, mutation, phenotype, pathway, and so on, which are the key scope of the data in the precision medicine (PM) knowledge base.

[cmungall]

Minor: download link should be to an uncompressed OWL file, not a rar

The major problem here is that scope is very broad, and it's not clear how this is distinguished from OGMS

[kang-hongyu]

Minor: download link should be to an uncompressed OWL file, not a rar

The major problem here is that scope is very broad, and it's not clear how this is distinguished from OGMS

PMO covers more fields of precision medicine than OGMS, for example Drug, Mutation, Gene, Cell and Biologic Function, while OGMS only focuses on Disease, Diagnosis, Carcinomas and other Pathological Entities.

What’s more, the currently uploaded rar version contains a large number of instances and related properties, while the owl version is too large to upload. If needed, we will adjust the ontology file for uploading again as soon as possible. Thanks very much.

[cmungall]

Can you also send an email to the obo-discuss list (with a link to this ticket) to bring in further discussion? Thanks!

On Mon, Jan 7, 2019 at 2:13 AM PMO notifications@github.com wrote:

Minor: download link should be to an uncompressed OWL file, not a rar

The major problem here is that scope is very broad, and it's not clear how this is distinguished from OGMS

PMO covers more fields of precision medicine than OGMS, for example Drug, Mutation, Gene, Cell and Biologic Function, while OGMS only focuses on Disease, Diagnosis, Carcinomas and other Pathological Entities. What’s more, the currently uploaded rar version contains a large number of instances and related properties, while the owl version is too large to upload. If needed, we will adjust the ontology file for uploading again as soon as possible. Thanks very much.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/815#issuecomment-451886252, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGOcVOFev6vInUcR8ffFUIH0oPX8y3ks5vAx3OgaJpZM4Znov4 .

[yongqunh]

The scope of this proposed PMO ontology has already been covered by the Ontology of Precision Medicine and Investigation (OPMI): http://www.obofoundry.org/ontology/opmi.html Therefore, I don’t think we need another precision medicine ontology.

The OPMI project is also currently supported by the NIH-supported Kidney Precision Medicine Project (KPMP): https://kpmp.org/ It is being actively developed and applied in the KPMP use case.

The OPMI project is open and welcome collaboration.

Best, Oliver

From: PMO [mailto:notifications@github.com] Sent: Thursday, January 03, 2019 1:52 AM To: OBOFoundry/OBOFoundry.github.io Cc: Subscribed Subject: [OBOFoundry/OBOFoundry.github.io] PMO prefix and PURL request (#815)

Requested Prefix: PMO

Ontology Title: The Precision Medicine Ontology

Download link: https://github.com/PMOntology/The-Precision-Medicine-Ontology/blob/master/PMO_sub.rar

Home page: https://github.com/PMOntology/The-Precision-Medicine-Ontology

Contact e-mail: kang.hongyu@imicams.ac.cnmailto:kang.hongyu@imicams.ac.cn

Tracker link: https://github.com/PMOntology/The-Precision-Medicine-Ontology/issues

Description: PMO is an extensible ontology aimed to integrate the terms in field of precision medicine, and all of the terms and relationships in PMO can apply in text mining or knowledge base building. PMO supports the identification and semantic integration of gene, disease, drug, mutation, phenotype, pathway, and so on, which are the key scope of the data in the precision medicine (PM) knowledge base.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/815, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEetQzy_DhMAmRUQzulVCkWtlz2oGKyDks5u_ah_gaJpZM4Znov4.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[kang-hongyu]

Can you also send an email to the obo-discuss list (with a link to this ticket) to bring in further discussion? Thanks! … On Mon, Jan 7, 2019 at 2:13 AM PMO @.***> wrote: Minor: download link should be to an uncompressed OWL file, not a rar The major problem here is that scope is very broad, and it's not clear how this is distinguished from OGMS PMO covers more fields of precision medicine than OGMS, for example Drug, Mutation, Gene, Cell and Biologic Function, while OGMS only focuses on Disease, Diagnosis, Carcinomas and other Pathological Entities. What’s more, the currently uploaded rar version contains a large number of instances and related properties, while the owl version is too large to upload. If needed, we will adjust the ontology file for uploading again as soon as possible. Thanks very much. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#815 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGOcVOFev6vInUcR8ffFUIH0oPX8y3ks5vAx3OgaJpZM4Znov4 .

We have uploaded a new OWL file and updataed the download link for our ontology, and sent an e-mail to the obo-discuss list.Thank you very much.

[kang-hongyu]

The scope of this proposed PMO ontology has already been covered by the Ontology of Precision Medicine and Investigation (OPMI): http://www.obofoundry.org/ontology/opmi.html Therefore, I don’t think we need another precision medicine ontology. The OPMI project is also currently supported by the NIH-supported Kidney Precision Medicine Project (KPMP): https://kpmp.org/ It is being actively developed and applied in the KPMP use case. The OPMI project is open and welcome collaboration. Best, Oliver From: PMO [mailto:notifications@github.com] Sent: Thursday, January 03, 2019 1:52 AM To: OBOFoundry/OBOFoundry.github.io Cc: Subscribed Subject: [OBOFoundry/OBOFoundry.github.io] PMO prefix and PURL request (#815) Requested Prefix: PMO Ontology Title: The Precision Medicine Ontology Download link: https://github.com/PMOntology/The-Precision-Medicine-Ontology/blob/master/PMO_sub.rar Home page: https://github.com/PMOntology/The-Precision-Medicine-Ontology Contact e-mail: kang.hongyu@imicams.ac.cnmailto:kang.hongyu@imicams.ac.cn Tracker link: https://github.com/PMOntology/The-Precision-Medicine-Ontology/issues Description: PMO is an extensible ontology aimed to integrate the terms in field of precision medicine, and all of the terms and relationships in PMO can apply in text mining or knowledge base building. PMO supports the identification and semantic integration of gene, disease, drug, mutation, phenotype, pathway, and so on, which are the key scope of the data in the precision medicine (PM) knowledge base. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#815>, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEetQzy_DhMAmRUQzulVCkWtlz2oGKyDks5u_ah_gaJpZM4Znov4. ** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Thank you for your comments. In our view，PMO is targeted at the whole field of precision medicine for scientific researchers and have covered the whole spectrum of diseases, rather than specific diseases.What ‘smore, PMO has more descriptions of class such as Biochemical pathways,Mutation and Gene from the class perspective of ontology than OPMI.

[yongqunh]

I was able to open PMO_obo_sub.owl in Protégé now： https://raw.githubusercontent.com/PMOntology/The-Precision-Medicine-Ontology/master/PMO_obo_sub.owl

The top level branches under PMO include:

• Anatomic Structure

• Biochemical Pathway

• Biological Function

• Cell

• Chemical and Drug

• Disease

• Gene

• Gene Product

• Mutation

• Phenotypic Abnormality

These areas have been more or less covered by different OBO ontologies. For example, Anatomic Structure by UBERON and FMA, Cell by Cell Ontology, etc.

One observation is that all the terms have their PMO IDs and then link to existing ontologies, for example, PMO “Phenotypic Abnormality” (http://www.PMO.com/PMO:00000866), which is linked to HPO:HP:0000118, MC01000368, and PMO:00000866. It appears that such a strategy does not follow the term reuse approach as OBO would propose.

From: PMO [mailto:notifications@github.com] Sent: Friday, January 18, 2019 4:40 AM To: OBOFoundry/OBOFoundry.github.io Cc: He, Oliver; Comment Subject: Re: [OBOFoundry/OBOFoundry.github.io] PMO prefix and PURL request (#815)

Can you also send an email to the obo-discuss list (with a link to this ticket) to bring in further discussion? Thanks! … On Mon, Jan 7, 2019 at 2:13 AM PMO @.***> wrote: Minor: download link should be to an uncompressed OWL file, not a rar The major problem here is that scope is very broad, and it's not clear how this is distinguished from OGMS PMO covers more fields of precision medicine than OGMS, for example Drug, Mutation, Gene, Cell and Biologic Function, while OGMS only focuses on Disease, Diagnosis, Carcinomas and other Pathological Entities. What’s more, the currently uploaded rar version contains a large number of instances and related properties, while the owl version is too large to upload. If needed, we will adjust the ontology file for uploading again as soon as possible. Thanks very much. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#815 (comment)https://github.com/OBOFoundry/OBOFoundry.github.io/issues/815#issuecomment-451886252>, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGOcVOFev6vInUcR8ffFUIH0oPX8y3ks5vAx3OgaJpZM4Znov4 .

We have uploaded a new OWL file and updataed the download link for our ontology, and sent an e-mail to the obo-discuss list.Thank you very much.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/OBOFoundry/OBOFoundry.github.io/issues/815#issuecomment-455485428, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AEetQ12p2zk4fa1xtmgrWSJG2vNWn6TQks5vEZZcgaJpZM4Znov4.

---

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[kang-hongyu]

There are some basic formatting errors in the submitted ontology file. Now we are modifying it and will update a new ontology file as soon as possible.Thank you for all the valuable advices.

[kang-hongyu]

We have uploaded a new version of ontology owl file, please check this time，thanks a lot.

Download link: https://raw.githubusercontent.com/PMOntology/The-Precision-Medicine-Ontology/master/PMO_obo_sub_v2.owl

[cmungall]

Thank you.

I have looked at the ontology. I agree with Oliver, but I would go further. It looks like you have taken MESH and redistributed it, with some slight modifications. In some cases (disease and phenotype), you have replaced by the primary ID/URI with an OBO one (DOID/HP). When you do replace the IDs, it looks like you leave the MESH structure in place.

For example, you include the HPO classes 'Abnormality of lower limb bone' and 'Abnormality of the lower limb' but you do not include the SubClassOf link between these, as HPO does.

There may be similar cases for DO, I have not checked. It does look like a fairly arbitrary subset of DO, with many of the most useful classes omitted.

In both cases, you are redistributing an arbitrarily restricted version of an existing ontology. While this is technically allowed for DO under its CC-0 license, I don't think we want to encourage this kind of arbitrary subsetting and modification. Note that the HPO has a more restrictive license which may disallow the kinds of modifications you are making.

I also think the name you have chosen "Precision Medicine Ontology" is not reflective of the scope. You do not have terms that are specific to the domain of PM. You are just redistributing parts of MESH with different IDs. You may want to choose a name that reflects this.

Note that MESH is not an OBO ontology and has different terms and conditions from most OBOs, you should check these: https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html

My recommendation is that this is not included in the OBO library. After you have clarified any licensing issues and chosen a more appropriate name, I think BioPortal may be a good home for this ontology.

On Sat, Feb 2, 2019 at 6:22 PM PMO notifications@github.com wrote:

We have uploaded a new version of ontology owl file, please check this time，thanks a lot.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/815#issuecomment-460016981, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGOQJk2_gZV31i8-GFzYpW451NiT9Hks5vJkfigaJpZM4Znov4 .

[kang-hongyu]

Thank you. I have looked at the ontology. I agree with Oliver, but I would go further. It looks like you have taken MESH and redistributed it, with some slight modifications. In some cases (disease and phenotype), you have replaced by the primary ID/URI with an OBO one (DOID/HP). When you do replace the IDs, it looks like you leave the MESH structure in place. For example, you include the HPO classes 'Abnormality of lower limb bone' and 'Abnormality of the lower limb' but you do not include the SubClassOf link between these, as HPO does. There may be similar cases for DO, I have not checked. It does look like a fairly arbitrary subset of DO, with many of the most useful classes omitted. In both cases, you are redistributing an arbitrarily restricted version of an existing ontology. While this is technically allowed for DO under its CC-0 license, I don't think we want to encourage this kind of arbitrary subsetting and modification. Note that the HPO has a more restrictive license which may disallow the kinds of modifications you are making. I also think the name you have chosen "Precision Medicine Ontology" is not reflective of the scope. You do not have terms that are specific to the domain of PM. You are just redistributing parts of MESH with different IDs. You may want to choose a name that reflects this. Note that MESH is not an OBO ontology and has different terms and conditions from most OBOs, you should check these: https://www.nlm.nih.gov/databases/download/terms_and_conditions_mesh.html My recommendation is that this is not included in the OBO library. After you have clarified any licensing issues and chosen a more appropriate name, I think BioPortal may be a good home for this ontology. … On Sat, Feb 2, 2019 at 6:22 PM PMO @.***> wrote: We have uploaded a new version of ontology owl file, please check this time，thanks a lot. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#815 (comment)>, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGOQJk2_gZV31i8-GFzYpW451NiT9Hks5vJkfigaJpZM4Znov4 .

Due to the required size of uploaded files, our uploaded version deletes the hierarchical relationship of the original PMO ontology which contains all the hierarchical relationships of HPO and other cases. Later, we will upload a new version based on your suggestion to supplement the hierarchical relationship as soon as possible. Thank you very much,

[pbuttigieg]

@PMOntology

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.