NTRs: document related publication

[zhengj2007]

VEuPathDB database needs following two terms to annotate the publication status.

Name	Value
Label	published document
Definition	A document that is published such as in a journal.
Parent	IAO_0000310 document
Definition source	EFO_0001796 published

Name	Value
Label	document in preparation for publication
Definition	A document that is in preparation for submission to be published.
Parent	IAO_0000310 document
Definition source	EFO_0001795 in preparation

IAO:0000311 publication (http://purl.obolibrary.org/obo/IAO_0000311) Definition: "A document that has been accepted by a publisher". However, IAO does not defined what is a publisher. So, it is not clear whether 'published document' is IAO:0000311 publication?

Hi, Larry @LEHunter, You are the term editor of IAO:0000311. Do you have any comments on it? Thanks!

The terms were submitted to OBI before. The related issue: https://github.com/obi-ontology/obi/issues/1091

[LEHunter]

For the former, we already have a term, e.g. IAO_0000013 (journal article). I agree we could use a new term for preprints or manuscripts in preparation. Probably also a subclass of IAO_0000088 (report) instead of its superclass IAO_0000310 (document).

Larry

On Oct 14, 2020, at 10:24 AM, jie zheng notifications@github.com wrote:

VEuPathDB https://veupathdb.org/ database needs following two terms to annotate the publication status.

Name Value Label published document Definition A document that is published such as in a journal. Parent IAO_0000310 document Definition source EFO_0001796 published Name Value Label document in preparation for publicaton Definition A document that is in preparation for submission to be published. Parent IAO_0000310 document Definition source EFO_0001795 in preparation IAO:0000311 publication (http://purl.obolibrary.org/obo/IAO_0000311 http://purl.obolibrary.org/obo/IAO_0000311) Definition: "A document that has been accepted by a publisher". However, IAO does not defined what is a publisher. So, it is not clear whether 'published document' is IAO:0000311 publication?

Hi, Larry @LEHunter https://github.com/LEHunter, You are the term editor of IAO:0000311. Do you have any comments on it? Thanks!

The terms were submitted to OBI before. The related issue: obi-ontology/obi#1091 https://github.com/obi-ontology/obi/issues/1091 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/information-artifact-ontology/IAO/issues/232, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACWZKKWJ2J2HLU7SQVRAR3SKXGCRANCNFSM4SQ2SMNA.

[zhengj2007]

I checked the IAO_0000088 (report). I think it fits better. We may consider to change the label to 'published report' as well if we want to change the parent.

'journal article' is an example of 'published document'.

We have proposed to add 'publishing process' and use equivalent axiom to define 'published document'.

Proposed definition for 'publishing process': Definition: A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Definition source: https://en.wikipedia.org/wiki/Publishing

'published document': Definition: A document that is published such as in a journal. Equivalent axiom: document and is_specified_output_of some 'publishing process' (not require a publisher)

Any thoughts and comments @LEHunter? Thanks!

Jie

[cstoeckert]

Discussed on OBI/IAO call Nov. 9, 2020. Agree to move forward with a 'publishing process' that would enable defining parts of the publishing process and the ouputs. Would address publication status.

AI: Jie move ahead with creating 'publishing process' as defined above.

[zhengj2007]

Added 'publishing process' with ID: IAO_0000444

[zhengj2007]

Proposed to update IAO:0000311 'publication' (http://purl.obolibrary.org/obo/IAO_0000311)

• Definition: A document that is published such as in a journal.

• Logical axiom (equivalent): document and is_specified_output_of only 'publishing process'

• Alternative term: published document

[zhengj2007]

Discussed on Nov 23, 2020 OBI call. Will make the changes and create pull request for Dr. Larry Hunter to review.

[LEHunter]

Is there a record of the discussion? I couldn’t join, and have a concern about the apparent disconnect between the logical and English definitions. An English definition that was similar to the logical one (e.g. “A document that has gone through a publication process”) would be better.

Larry

On Nov 23, 2020, at 8:07 AM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

Discussed on Nov 23, 2020 OBI call. Will make the changes and create pull request for Dr. Larry Hunter to review.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/information-artifact-ontology/IAO/issues/232#issuecomment-732332513, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AACWZKNZJI6Z5JK4B3MGRJLSRKQHNANCNFSM4SQ2SMNA.

[zhengj2007]

I changed the definition back to 'A document that is published such as in a journal.', which is agreed before. The one that fits the updated logical definition you proposed looks fine to me.

[zhengj2007]

@LEHunter How about this?

proposed definition for publication: "A document that has gone through a publishing process, such as journal article."

[LEHunter]

I like that better. How about “A document that is the output of a publishing process.” Then in "example of usage," you could list journal article, newspaper story, book, etc.

Larry

On Nov 23, 2020, at 8:18 AM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@LEHunterhttps://github.com/LEHunter How about this?

proposed definition for publication: "A document that has gone through a publishing process, such as journal article."

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/information-artifact-ontology/IAO/issues/232#issuecomment-732338629, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AACWZKOCI5XDR6YRWXC7EX3SRKRORANCNFSM4SQ2SMNA.

[zhengj2007]

Updated IAO_0000311 publication: Definition: A document that is the output of a publishing process. example of usage: journal article, newspaper story, book, etc. alternative term: published document

Added term 'document in preparation for publication', assigned ID: IAO_0000445

[LEHunter]

I approve of the definition.

On Nov 23, 2020, at 1:54 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

Updated IAO_0000311 publication: Definition: A document that is the output of a publishing process. example of usage: journal article, newspaper story, book, etc. alternative term: published document

Added term 'document in preparation for publication', assigned ID: IAO_0000445

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/information-artifact-ontology/IAO/issues/232#issuecomment-732493120, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AACWZKNULRHPTFFMTKLATR3SRLY2BANCNFSM4SQ2SMNA.

[zhengj2007]

Thanks @LEHunter

[zhengj2007]

The new term and updated 'publication' term are available in release 2020-12-09.