New OpenLifeData services

[Mark Wilkinson]

Hi all,

Just a quick update on the available SADI services:

I have done two things in the past week:

1) I pruned the registry of any services that don't respond *at
all* (they may not respond correctly, but at least the service still
advertises to be alive)

2) I deleted all of the existing OpenLifeData services and replaced
them with new services that work from Michel's new, consolidated
OpenLifeData endpoint. It will take about 12 hours for all of the new
services to register, so please be patient. You can browse the registry
using my new (ugly, but functional) registry browser:
http://sadiframework.org/registry/services



*Details about the new OpenLifeData services*

Number of services removed: ~22,000
Number of services added: ~40,000
Bio2RDF Namespaces Served: affymetrix apo drugbank eco go goa hgnc
homologene hp irefindex kegg mesh mgi omim sgd sider taxonomy
wormbase
Notes:
1) The services only operate in the "forward direction" v.v. ?s ?p
?o. Hopefully this afternoon I will have finished updating the scripts
to create the inverse services also. This will add ~10-15% more
services (since I cannot invert services that have a datatype predicate,
which is most of the OpenLifeData services)
2) The other thing I plan to do is to automatically add exemplar
input data to each service's interface definition. There is a place for
this exemplar data in the mygrid-moby ontology, and we used it for the
BioMoby project to enable automated service testing "back in the old
days". We will soon be able to do that for the OpenLifeData services
too! Hopefully I can do this during this week, but it might be longer
since it requires an update to the core SADI service codebase.


*Example for you to try*:

SERVICE ENDPOINT:
http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/go/chebi_vocabulary_Resource_terms_identifier

INPUT (sampledata.chebi):

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">

<rdf:Description rdf:about="http://bio2rdf.org/chebi:15354">

<rdf:type rdf:resource="http://bio2rdf.org/chebi_vocabulary:Resource"/>

</rdf:Description>

</rdf:RDF>


TO EXECUTE FROM COMMAND LINE:
curl --data-binary @sampledata.chebi
'http://biordf.org/cgi-bin/SADI/OpenLifeData2SADI/SADI/go/chebi_vocabulary_Resource_terms_identifier'


Cheers all!

Mark

[Michel Dumontier]

Great!
Can you add a link to download "all" service descriptions?
m.
Michel Dumontier
Associate Professor of Medicine (Biomedical Informatics), Stanford University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com

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[Mark Wilkinson]

On 02/23/2016 11:18 PM, Michel Dumontier wrote:
> Great!
> Can you add a link to download "all" service descriptions?

There isn't one.

You can browse all registry entries of the openlifedata services using
the registry browser, though.

M