DINTO

[GoogleCodeExporter]

Dear OBO Foundry members,

We have extended the first version of the Drug-Drug Interactions Ontology 
(DINTO). DINTO 1.2 includes information about adverse drug reactions (ADRs) and 
their relationships to pharmacological entities included in the ontology.

To create this version, we have imported a reduced version of the Ontology for 
Adverse Events  (OAE version 1.1.247), including only the top class 'adverse 
event' and its subclasses. This reduced subset of OAE can be downloaded from 
https://drive.google.com/folderview?id=0B-7Po9tR1KLUUDZPRkFGOFFmVjA&usp=sharing.

In addition to this, we have imported drug-ADR relationships for the database 
SIDER , which can be used with SWRL rules to infer DDIs occurring by the 
addition of a common ADR.

We would like to request the review of this new realease by the OBO Foundry, 
and the update of this version instead of the previous one at the OBO Foundry 
website.

DINTO 1.2 can be downloaded from https://code.google.com/p/dinto/

Description of the resource to review:

-ontology name: The Drug-Drug Interactions Ontology (DINTO)

-contact person name: Maria Herrero

-contact person email: asmarahz84@gmail.com; mariahz@pa.uc3m.es

-scope of ontology: Drug-drug interactions and related aspects

-link to stable version of the ontology:https://code.google.com/p/dinto/

-link to ontology documentation (e.g., web or wiki 
page):https://code.google.com/p/dinto/

-other important links (describe):-

-date of previous review request (if applicable):-

Kind regards,

María

Original issue reported on code.google.com by mhzazo@gmail.com on 16 Jun 2015 at 4:32

[GoogleCodeExporter]

Maria: 

We strongly suggest that you move the DINTO repository off of Google Code 
(http://google-opensource.blogspot.ca/2015/03/farewell-to-google-code.html) and 
onto another site such as Github. We do not want the migration to delay the 
review, so we are willing to start the review process during migration. 
However, we do not want to be in the situation of having the links to the 
ontology disappear just as we are working on the review!

Ramona

Original comment by rlwalls2...@gmail.com on 21 Jul 2015 at 4:03

[GoogleCodeExporter]

Original comment by rlwalls2...@gmail.com on 21 Jul 2015 at 4:03

• Changed state: Accepted

[GoogleCodeExporter]

Maria:

1. Are you requesting a formal review of DINTO, or do you simply want to update 
the links on the Foundry Website?

2. In order to have the OBO Foundry website link to the newest version of the 
ontology, you must update the PURL at purl.org. You or someone in your 
organization should have a login to administer DINTO PURLs.

3. In order for your ontology to pass review, it must exist on a version 
control system. Although you have set up a Google Code site for DINTO, it does 
not include a repository. We do not require a specific version control system, 
but it is unlikely that we would approve Google Drive as an adequate versioning 
system during review. Please consider moving your an established system like 
GitHub or Bitbucket. Many OBO Foundry ontology developers use Github and find 
it helpful for ontology development.

Original comment by rlwalls2...@gmail.com on 4 Aug 2015 at 11:20

[GoogleCodeExporter]

Original comment by rlwalls2...@gmail.com on 4 Aug 2015 at 11:21

[ramonawalls]

Comment from MHerrero that was made on Google Code after the migration:

Hello,

I will answer to your questions below:

1.Yes, we would like to request a formal review of DINTO.

1. Could you please let me know if I should create a new purl for the version 1.2, or modify the existing one?
2. We will move the DINTO repository to GitHub, as you suggested.

Thank you very much,

Maria

[ramonawalls]

Maria - Please paste the link to the new ontology repo here. As for the PURLS, you can continue to point the PURLs for older versions to your old repo, but I suggest that you move them to your new repo and redirect the PURLs there. There should be a separate PURL for each release (i.e. version). See this page (http://obofoundry.github.io/id-policy.html) for more details.

[labda]

Hello,

The link to the new ontology repo is: https://github.com/labda/DINTO

We have modified the PURL, so it redirects to the github repository.

We have created PURLS for the two versions: http://purl.obolibrary.org/obo/dinto/2014-06-25/dinto.owl http://purl.obolibrary.org/obo/dinto/2015-06-01/dinto.owl

Please, let us know any further step,

Kind regards,

Maria

[ramonawalls]

Thanks for the update. Normally, the PURLs for both versions should point directly to the raw version of the file, so they can be opened directly from the PURL. For example: http://purl.obolibrary.org/obo/dinto/2014-06-25/dinto.owl should point to https://raw.githubusercontent.com/labda/DINTO/master/DINTO%201/DINTO_1.owl

However, I see this is a problem with version 2, because it the files may be too large for Github and you are currently storing it as a zipped file. Even version 1 cannot be opened in Protege directly from the URL. In this case, maybe Github is not the ideal repository for your files.

Is there a reason that the ontology is so large? Are you importing a lot of large external ontologies? Is it just because you have so many classes? A better approach might be to make the ontology modular, so that the main ontology just includes DINTO classes and scripts to import external files (like the OAE subset).

[ramonawalls]

A preliminary review suggested that DINTO does not comply adequately with some of the OBO Foundry principles. We have asked the developers to make some changes and re-do the self-assessment when they are ready.

Closing this issue for now. Will re-open when a new self-assessment is submitted.

[ramonawalls]

See pre-review at https://docs.google.com/document/d/16ZCwEmWuv9eYzilm0VKPb-QjupKfn5l_R7RZVlIryTs/edit