replace ERO with VIVO-ISF

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Hi there,

The VIVO ontology and the eagle-i resource ontology (ERO) have been merged into 
what is now called the VIVO-ISF ontology. 

Can we mark ERO as no longer under active development and instead register 
VIVO-ISF as having replaced/subsumed it?

Here is the Project info page for VIVO-ISF:
https://wiki.duraspace.org/display/VIVO/VIVO-ISF+Ontology

Releases:
https://connect-isf.googlecode.com/svn/release/
https://connect-isf.googlecode.com/svn/release/2013-07-31/isf.owl

Development version:
https://connect-isf.googlecode.com/svn/trunk/src/ontology/isf-dev.owl

Description:
VIVO-ISF subsumes the eagle-i resource ontology, modeling research resources 
such instruments. protocols, reagents, animal models and biospecimens 
(http://eagle-i.net/). It has been merged and extended in the context of the 
VIVO ontology (www.vivoweb.org), which represents people and their activities. 
The goal is to relate scholarly products of research to people, grants, and 
publications for research profiling and science of team science.

I'll admit I am not quite sure what to do with the PURLs as some content is 
outside the Foundry, but Oliver is loading into Ontobee so we can start with 
that. 

Thanks,
Melissa

Original issue reported on code.google.com by haen...@ohsu.edu on 18 Mar 2014 at 3:45

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Hi Melissa,

Sorry I didn't quite get the end of your message "I'll admit I am not quite 
sure what to do with the PURLs as some content is outside the Foundry, but 
Oliver is loading into Ontobee so we can start with that. "
Could you expand?

Regarding replacing ERO by VIVO-ISF, that shouldn't be an issue, however as far 
as I know when we mark ERO as deprecated it won't show up in the table anymore. 
Also there are no mechanisms to indicate "VIVO-ISF replaces ERO" but for the 
textual description you provided.

Cheers,
Melanie

Original comment by mcour...@gmail.com on 5 Jun 2014 at 11:11

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1. Update the ontologies.txt by copy/pasting the ERO entry, modifying it to be 
VIVO-ISF per 
2. Add is_obsolete true and replaced_by VIVO_ISF to the old entry
example is UBERON replacing some other anatomy ontologies
3. add status Inactive

OOPS there is an issue.
The ontology pointed has URL 
http://purl.obolibrary.org/obo/isf.owl
Ontologies are using e.g. http://purl.obolibrary.org/obo/ARG_2000391

a) ARG is not a registered namespace
b) is it intended that the namespace be ARG? If not, then please stop using 
purls in that namespace. If you plan to continue using them you *must* register 
ARG.
c) If we register ARG, what title do you want to associate with the project 
"VIVO_ISF" or something longer?
d) registering VIVO_ISF would mean that the purls would be  
http://purl.obolibrary.org/obo/VIVO_ISF_2000391 and we would expect 
http://purl.obolibrary.org/obo/arg.owl to be the ontology URL.  Do you want to 
register ISF instead? Are you planning to deprecate all the ERO_ ids? (would be 
uncool). There appear to be ERO_ids in the current files which suggest that the 
ERO namespace will continue to exist.  

Bottom line: We need to get more information and clarification. The current 
metadata is below. Do you just mean to change the metadata for ERO description?

id  ero
title   eagle-i resource ontology
namespace   ERO
foundry No
metadata_ontology   IAO
status  Production and review
download     http://purl.obolibrary.org/obo/ero.owl
source  
home    http://code.google.com/p/eagle-i/
documentation   http://code.google.com/p/eagle-i/wiki/Documentation
contact Carlo Torniai   carlotorniai    gmail.com 
format  owl
description ERO models research resources such instruments. protocols, 
reagents, animal models and biospecimens. It has been developed in the context 
of the eagle-i project  (http://eagle-i.net/).
domain  resources

Original comment by alanruttenberg@gmail.com on 10 Jun 2014 at 6:50

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It also seems I was wrong - we can mark resources as inactive, and it wouldn't 
disappear. There is also a replaced_by tag that can be used.

Original comment by mcour...@gmail.com on 10 Jun 2014 at 6:52

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Correction (updated name of ontology in example)
d) registering VIVO_ISF would mean that the purls would be  
http://purl.obolibrary.org/obo/VIVO_ISF_2000391 
and we would expect http://purl.obolibrary.org/obo/vivo_isf.owl to be the 
ontology URL.  Do you want to register ISF instead? Are you planning to 
deprecate all the ERO_ ids? (would be uncool). There appear to be ERO_ids in 
the current files which suggest that the ERO namespace will continue to exist.  

Original comment by alanruttenberg@gmail.com on 10 Jun 2014 at 6:52

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Note that the /obo/arg already exists (maintained by Carlo, Alan and Chris)

Original comment by mcour...@gmail.com on 15 Jun 2014 at 2:42