INOH BioPAX Level2 release now available.

[Ken Fukuda]

Hi there,

All INOH pathway diagram files are now available in BioPAX Level2 format.

Visit Download page and get each file separately or as a single archive.
http://www.inoh.org/download.html#PathwayData

Release note:

Known issues:

1. There are some instances not referred from any instances.
(undeleted garbage generated during the conversion)
* Some "INOH_GID_LID"s of "unificationXref".
* "Connected_xxx" of "relationshipXref"
* "PASSING_xxx"
* Some "phsicalEntityParticipant"s
e.g.) MI0006343_IkB_NFkB0_pep(B_cell_receptor_signaling.owl)

2. Mapped to COMMENT property (should be resolved in the next level of BioPAX)
* Amino residue names (e.g. Ser), domain names (e.g. ITAM) in
SequenceFeature mapped to COMMENT of sequenceFeature
* Evidence information of Material nodes mapped to COMMENT of PEP or SP
* Connected edge information mapped to COMMENT of relationshipXref
class's instances "Connected_xxx"

Best,
Ken

---------------------------------------------
Ken Ichiro Fukuda, Ph.D.
Computational Biology Research Center (CBRC)
National Institute of
Advanced Industrial Science and Technology (AIST)
AIST Tokyo Waterfront Bio-IT Research Bldg.
2-42 Aomi, Koutou-ku, Tokyo 135-0064 JAPAN
Phone: +81-3-3599-8049 FAX: +81-3-3599-8081
fukud...@aist.go.jp
- http://www.cbrc.jp/~fukuda/index.html
- INOH Pathway Database Project -
- Integrating Network Objects with Hierarchies
- http://www.inoh.org

[Gary Bader]

That's great Ken! We're testing it with cPath and Cytoscape now and
will send you feedback.

Thanks,
Gary

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Terrence Donnelly Centre for Cellular and Biomolecular Research
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