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NIF Standard Ontologies (NIFSTD)
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Transition to Scicrunch and re-use of NeuroLex terms #31

Closed cmaumet closed 8 years ago

cmaumet commented 8 years ago

Hello,

I was wondering if you could provide us with some inputs on the best practice to re-use a NeuroLex term following transition to SciCrunch?

We are currently using NeuroLex terms as part of the NeuroImaging Data Model (http://nidm.nidash.org). For instance, we use the term "SPM" with the following URI: http://neurolex.org/wiki/nif-0000-00343 (e.g. example001_spm_results.ttl). But when looking up "SPM" on SciCrunch, the main identifier for this term is SCR_007037 while nif-0000-00343 is listed as an alternate id.

So, I was wondering if:

Thank you in advance for your feedback!

tgbugs commented 8 years ago

1) Please use the SCR identifiers. 2) The prefix that I am planning to use for SCR identifiers is http://scicrunch.org/resolver/ with the curie mapping being 'SCR':'http://scicrunch.org/resolver/SCR_'. For your example: http://scicrunch.org/resolver/SCR_007037

There will be a full ttl export of the scicrunch registry done weekly that will eventually live here (currently a broken link). The code to generate it is here though it will not run since the database requires password access.

Let me know if you have other questions. Thanks!

yul129 commented 8 years ago

Please find below answers to your questions.

SciCrunch ids will be the ids for both new resources and existing resources and original ids will also been documented as alternative id for existing resources. It is OK to keep the original ids in your documents but for the new entries in the future, there will only be SciCrunch ids.

The URL structure for Scr based ids is https://scicrunch.org/browse/resources/SCR_XXXXXXhttps://scicrunch.org/browse/resources/SCR_007037

From: Camille Maumet [notifications@github.com] Sent: Tuesday, February 02, 2016 8:30 AM To: SciCrunch/NIF-Ontology Subject: [NIF-Ontology] Transition to Scicrunch and re-use of NeuroLex terms (#31)

Hello,

I was wondering if you could provide us with some inputs on the best practice to re-use a NeuroLex term following transition to SciCrunch?

We are currently using NeuroLex terms as part of the NeuroImaging Data Model (http://nidm.nidash.org). For instance, we use the term "SPM" with the following URI: http://neurolex.org/wiki/nif-0000-00343 (e.g. example001_spm_results.ttlhttps://github.com/incf-nidash/nidm/blob/master/nidm/nidm-results/spm/example001/example001_spm_results.ttl#L119). But when looking up "SPM" on SciCrunchhttps://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/ba2e10d5-6149-55de-8cad-c72daaa08087/search?q=spm&l=, the main identifier for this term is SCR_007037 while nif-0000-00343 is listed as an alternate id.

So, I was wondering if:

Thank you in advance for your feedback!

— Reply to this email directly or view it on GitHubhttps://github.com/SciCrunch/NIF-Ontology/issues/31.

tgbugs commented 8 years ago

Opps broken link. It seems the url structure we want is http://scicrunch.org/browse/resources/SCR_007037. Looks like I will need to update on my end as well. However, I might still suggest the resolver since that will not change even if we fiddle with our urls in the future. Do we have a wiki/docs for this lurking somewhere? I will get a better answer asap.

jgrethe commented 8 years ago

Yueling - Tom responded already.

Cheers, Jeff

On Feb 2, 2016, at 9:54 AM, yul129 notifications@github.com wrote:

Please find below answers to your questions.

  • you would advice using the main SciCrunch ids (starting with SCR_) instead of the original ones (from NeuroLex) in our documents?

SciCrunch ids will be the ids for both new resources and existing resources and original ids will also been documented as alternative id for existing resources. It is OK to keep the original ids in your documents but for the new entries in the future, there will only be SciCrunch ids.

The URL structure for Scr based ids is https://scicrunch.org/browse/resources/SCR_XXXXXXhttps://scicrunch.org/browse/resources/SCR_007037

From: Camille Maumet [notifications@github.com] Sent: Tuesday, February 02, 2016 8:30 AM To: SciCrunch/NIF-Ontology Subject: [NIF-Ontology] Transition to Scicrunch and re-use of NeuroLex terms (#31)

Hello,

I was wondering if you could provide us with some inputs on the best practice to re-use a NeuroLex term following transition to SciCrunch?

We are currently using NeuroLex terms as part of the NeuroImaging Data Model (http://nidm.nidash.org). For instance, we use the term "SPM" with the following URI: http://neurolex.org/wiki/nif-0000-00343 (e.g. example001_spm_results.ttlhttps://github.com/incf-nidash/nidm/blob/master/nidm/nidm-results/spm/example001/example001_spm_results.ttl#L119). But when looking up "SPM" on SciCrunchhttps://scicrunch.org/scicrunch/Resources/record/nlx_144509-1/ba2e10d5-6149-55de-8cad-c72daaa08087/search?q=spm&l=, the main identifier for this term is SCR_007037 while nif-0000-00343 is listed as an alternate id.

So, I was wondering if:

Thank you in advance for your feedback!

— Reply to this email directly or view it on GitHubhttps://github.com/SciCrunch/NIF-Ontology/issues/31. — Reply to this email directly or view it on GitHub https://github.com/SciCrunch/NIF-Ontology/issues/31#issuecomment-178718051.

Jeffrey S. Grethe, Ph.D. email: jgrethe@ncmir.ucsd.edu mailto:jgrethe@ncmir.ucsd.edu
University of California, San Diego 9500 Gilman Drive, M/C 0608 La Jolla, CA 92093-0608

work: (858) 822-0703 ( fax: (858) 246-0644 http://orcid.org/0000-0001-5212-7052 http://crbs.ucsd.edu/ http://www.linkedin.com/in/jgrethe http://www.linkedin.com/in/jgrethe

This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

jgrethe commented 8 years ago

Hi Tom, Shouldn’t be browse-resources… Should be a resolver address - as that can be fixed. NeuroLex had the uri.neuinfo.org/ID format. We can do something similar for SciCrunch and InterLex.

On Feb 2, 2016, at 10:01 AM, Tom Gillespie notifications@github.com wrote:

Opps broken link. It seems the url structure we want is http://scicrunch.org/browse/resources/SCR_007037 http://scicrunch.org/browse/resources/SCR_007037. Looks like I will need to update on my end as well. However, I might still suggest the resolver since that will not change even if we fiddle with our urls in the future. Do we have a wiki/docs for this lurking somewhere? I will get a better answer asap.

— Reply to this email directly or view it on GitHub https://github.com/SciCrunch/NIF-Ontology/issues/31#issuecomment-178723454.

Jeffrey S. Grethe, Ph.D. email: jgrethe@ncmir.ucsd.edu mailto:jgrethe@ncmir.ucsd.edu
University of California, San Diego 9500 Gilman Drive, M/C 0608 La Jolla, CA 92093-0608

work: (858) 822-0703 ( fax: (858) 246-0644 http://orcid.org/0000-0001-5212-7052 http://crbs.ucsd.edu/ http://www.linkedin.com/in/jgrethe http://www.linkedin.com/in/jgrethe

This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

cmaumet commented 8 years ago

Thank you very much for your replies!

So, just to confirm, the URIs for SciCrunch terms will have the following form: http://scicrunch.org/resolver/SCR_*** ?

I know this is work-in-progress but could you confirm whether you plan to have a SCR_ *** id for each NeuroLex term (including the ones that were not part of the Resource Identification Initiative)? E.g. nlx:nlx_inv_090912 ("Magnetic resonance imaging"). If so and if there is a place where we could look up the SRC_*** ids that have already been assigned please let us know.

For information, in addition to the software (FSL, SPM, AFNI) terms, we are planning to re-use:

tgbugs commented 8 years ago

Yes http://scicrunch.org/resolver/SCR_*** is preferred. We want to provide a http://resolver.scicrunch.org/SCR_*** in the future but links with that structure will 404 at the moment.

For other neurolex terms please use http://uri.neuinfo.org/nif/nifstd/ as your iri prefix (namespace). As we start moving terms out of neurolex and into nifstd that resolver will be updated so that it redirects to the most recent version of the term.

satra commented 8 years ago

@tgbugs and @jgrethe - would it be possible to introduce a sameAs property for any of the scicrunch or interlex terms that are taking over the older neurolex terms?

this would at least help resolve things given the older IRIs will go away. on our side we can try to add information to indicate that queries should take sameAs into account.

jgrethe commented 8 years ago

Yes. We have done that for the public resolver for resources and these could be incorporated into the ontology as well.

Cheers, Jeff

On Feb 3, 2016, at 5:24 AM, Satrajit Ghosh notifications@github.com wrote:

@tgbugs https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_tgbugs&d=CwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=VoBnXVyFWlbGZNrES22a2h0PqI4m1kGEUyTwLwBBYIQ&m=yGFbOjBBfz6T3rHBIMFZPY9dRkpcYefuCkSqDQNtJPQ&s=AEJCWv1sMJ4JYfCmWysDTZa3pLDxWAqJiY6y4WO76MU&e= and @jgrethe https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jgrethe&d=CwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=VoBnXVyFWlbGZNrES22a2h0PqI4m1kGEUyTwLwBBYIQ&m=yGFbOjBBfz6T3rHBIMFZPY9dRkpcYefuCkSqDQNtJPQ&s=zvSktdG3cJ_krM4JIfDbk_3SQrjImuorSOqLXKUlKXU&e= - would it be possible to introduce a sameAs property for any of the scicrunch or interlex terms that are taking over the older neurolex terms?

this would at least help resolve things given the older IRIs will go away. on our side we can try to add information to indicate that queries should take sameAs into account.

— Reply to this email directly or view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_SciCrunch_NIF-2DOntology_issues_31-23issuecomment-2D179226979&d=CwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=VoBnXVyFWlbGZNrES22a2h0PqI4m1kGEUyTwLwBBYIQ&m=yGFbOjBBfz6T3rHBIMFZPY9dRkpcYefuCkSqDQNtJPQ&s=Q78eLQWNaqr2BXz9cHFrCUR87BVJLlWcCR3mQLw8uq8&e=.

Jeffrey S. Grethe, Ph.D. email: jgrethe@ncmir.ucsd.edu mailto:jgrethe@ncmir.ucsd.edu
University of California, San Diego 9500 Gilman Drive, M/C 0608 La Jolla, CA 92093-0608

work: (858) 822-0703 ( fax: (858) 246-0644 http://orcid.org/0000-0001-5212-7052 http://crbs.ucsd.edu/ http://www.linkedin.com/in/jgrethe http://www.linkedin.com/in/jgrethe

This e-mail/fax message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail/fax and destroy all copies of the original message.

tgbugs commented 8 years ago

@satra I will include some form of a sameAs property in my export of the resource registry as well. I am currently exporting it as an an annotation property but could easily change it to an object property if that would make your life easier.

cmaumet commented 8 years ago

Thank you for your feedback! From now on, we will use the http://scicrunch.org/resolver/ and http://uri.neuinfo.org/nif/nifstd/ namespaces as suggested, this update is implemented in https://github.com/incf-nidash/nidm/pull/374.

I have open #34 to discuss more specific term re-use. I think that the discussions can continue over there and that we can close this issue.

tgbugs commented 8 years ago

Will close after I add a wiki page that covers this.

tgbugs commented 8 years ago

https://github.com/SciCrunch/NIF-Ontology/wiki/Identifiers-for-existing-terms https://github.com/SciCrunch/NIF-Ontology/wiki/Identifiers-for-research-resources https://github.com/SciCrunch/NIF-Ontology/wiki/Identifiers-for-new-terms