support- question regarding adding in ontologies/controlled vocab

[Yu Liu]

Hi ISA Creators and Users,

I'm not sure where to put this post but I'm trying to find out if
there is anyway to set up ISA configurator/creator so that custom
ontologies can be added in? We're trying to add in controlled vocab
with our own definitions and also SNOMED and MEDRA into the ontologies
list.

Another question was, the standard configuration by ISA configurator
for study table and assay table comes with Sample Name, Assay Name,
Raw Data File, etc. Is there anyway to set up a custom assay and
sample definition without the standard elements and only add in custom
elements with my naming conventions?

Please let me know if my wording is too confusing! I'm currently
trying to curtail isa tools at work but the standard templates/
definitions and ontologies are a little different from what I need.

Thanks for all your time and help!
David Liu

[Philippe Rocca-Serra]

Hi David,

Thanks for your post.
At the moment, only resources served by NCBO's Bioportal and EBI's
Ontology Lookup Service are available.
We have received requests from several groups to enable support of
local/custom resources.
This is something we are currently working on but we would probably
support OWL and OBO resources.
I believe sending a request to NCBO to investigation whether they would
be willing to host private resource would be interesting.

Regarding your second question (adding assay tables), the
ISAconfigurator should be used.
We are currently working on i.) refining the existing configurations for
a number of assays. ii.) gauge needs in terms of supporting other type
of assays.
We have prototype configurations for flow cytometry and working on other
domains.

Ideally, we would like to reach some level of agreement with communities
(work with the MIBBI project) to ensure consistent level of annotation.

But it seems that you need extension, beyond the existing ISA element.
Actually discussing why those are not enough in your use case would be
great.

Cheers

Philippe

[ball...@gmail.com]

I am curious if this functionality (adding custom ontologies) is still in the works.

[Alejandra Gonzalez-Beltran]

Hi,

The solution that different groups have adopted for custom ontology lookup is to create a plugin for ISAcreator (relying on the OSGi framework).

A couple of examples you can consider are:

- the ToxBank plugin:

http://toxbank.net/tutorials/isa-tab/2-6-isa-tab-technical-information

- the Novartis Metastore:
https://github.com/ISA-tools/NovartisMetastore

HTH,

Alejandra

--
--
--
 
You received this message because you are subscribed to the Google
Groups "ISAforum" group.
To post to this group, send email to isaf...@googlegroups.com
To unsubscribe from this group, send email to
isaforum+u...@googlegroups.com
For more options, visit this group at
http://groups.google.com/group/isaforum?hl=en-GB
 
Visit the ISAtools website at http://isa-tools.org

---
You received this message because you are subscribed to the Google Groups "ISAforum" group.
To unsubscribe from this group and stop receiving emails from it, send an email to isaforum+u...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.