[MOBY-dev] Re: [MISC] hi

[Mark Wilkinson]

Dear GO Consortium members, 

I am writing to you as project leader of the BioMOBY interoperability
project - an open-source project aimed at building a  platform for the
representation, discovery, and transaction of biological data services.
One of the ontologies that we require in this project is a "Namespace"
ontology; this is effectively an ontology of various data types as
represented by common ID numbers.  The Namespace Ontology maps
conceptually onto the existing Gene Ontology Cross-Reference
Abbreviations List, where you enumerate all of the different "prefixes"
that are assigned to GO Xref's (e.g. NCBI_gi is the abbreviation for
genbank records).  Rather than create a list of our own de novo, we have
imported the existing GO Xref Abbs into our ontology, however since MOBY
is currently representing data-types that are not part of your  Xref
Abbs list, we have extended this list to include additional Namespaces
that we require.  We have also extended the specification such that each
Namespace can be represented by a Life Sciences Identifier (LSID), and
have set up an LSID meta-data resolution service on our project's server
that is freely publicly accessible.

It seems to me that it would be a shame (and a curatorial headache) to
have two public lists of Namespaces that are not in-sync with each
other.  As such, I have raised with Michael Ashburner the possibility
that the BioMOBY project take over the task of maintaining and curating
this list, since we appear to edit it more frequently than you do.  This
came with several proviso's:

1)  that we continue to offer all the data completely freely, both to
you and everyone else.
2)  that we build an interface (or make a regular dump) to provide you
the data in the current GO Xrefs Abbs file format such that we do not
break any of your existing tools
3)  that we promise to give you back all relevant data and scripts in
the event that the BioMOBY project expires for any reason.

I hope that you will consider this and make a favourable decision!  If
there are any additional provisions, please let me know as I am certain
that we can accommodate them.

Sincerely, 

Mark Wilkinson


-- 
Mark Wilkinson <markw at illuminae.com>
Illuminae