couple more things about INOH Biopax

Alan Ruttenberg

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Jun 1, 2006, 12:21:51 AM6/1/06

to Ken I Fukuda, BioPAX Manchester

Hi Ken,

Some more stuff:

These are direct instances of owl:Thing, which usually means that
they are referred to somewhere, but not defined anywhere (pellet says
they must be *something* so it makes them instances of owl:Thing)

Connected_id1657654683_id1285092580,
Connected_id997589207_id46795497, Connected_id625026951_id1588707703,
id699451362_Smad7, Connected_id121677340_id33496024, !<http://
www.biopax.org/release/Proteasome%20degradation>,
Connected_id1165069402_id1936035698, id1387703047_Transcription0,
Connected_id1350648522_id114353630,
Connected_id1165069402_id1709918560,
Connected_id1350648522_id1588707703, id687446721_Transcription0,
Connected_id997589207_id114353630,
Connected_id1657654683_id1709918560, id559533476_Smad7,
Connected_id625026951_id1200991115, Connected_id121677340_id933799551

In addition there are many unification xrefs

<unificationXref rdf:ID="IEV_0000010">
<DB rdf:datatype="http://www.w3.org/2001/
XMLSchema#string">IEV_0000010</DB>
<ID rdf:datatype="http://www.w3.org/2001/
XMLSchema#string">Proteasome degradation</ID>
<COMMENT rdf:datatype="http://www.w3.org/2001/
XMLSchema#string">http://www.inoh.org (ProcessOntology)</COMMENT>
</unificationXref>

In these, I think that the DB should be something like "INOH Process
Ontology"(or better a definitive URL for the the process ontology),
and the ID IEV_0000010 and the comment (or better the rdfs:label)
"Proteasome degradation"

Finally, if you add something like this:

<!DOCTYPE rdf:RDF [
<!ENTITY owl "http://www.w3.org/2002/07/owl#">
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
]>

at the beginning of your file between the first two lines:

<?xml version="1.0" encoding="UTF-8"?>
************** over here *************
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"

you will be able to abbreviate

to

to make the file a bit shorter.

Later,
Alan

Ken I Fukuda

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Jun 1, 2006, 12:47:31 AM6/1/06

to Alan Ruttenberg, BioPAX Manchester

Hi,

Thanks for the feadback. Will check and comment on this
soon.

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. 10F
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

Ken I Fukuda

unread,

Jun 1, 2006, 1:35:46 PM6/1/06

to Alan Ruttenberg, BioPAX Manchester

Hi,

> These are direct instances of owl:Thing, which usually means that
> they are referred to somewhere, but not defined anywhere (pellet says
> they must be *something* so it makes them instances of owl:Thing)
>
> Connected_id1657654683_id1285092580,
> Connected_id997589207_id46795497, Connected_id625026951_id1588707703,
> id699451362_Smad7, Connected_id121677340_id33496024, !<http://
> www.biopax.org/release/Proteasome%20degradation>,
> Connected_id1165069402_id1936035698, id1387703047_Transcription0,
> Connected_id1350648522_id114353630,
> Connected_id1165069402_id1709918560,
> Connected_id1350648522_id1588707703, id687446721_Transcription0,
> Connected_id997589207_id114353630,
> Connected_id1657654683_id1709918560, id559533476_Smad7,
> Connected_id625026951_id1200991115, Connected_id121677340_id933799551

This is a bug and has been fixed.
They should are instances of sequence features.
I will send the fixed version later.

> In addition there are many unification xrefs
>
> <unificationXref rdf:ID="IEV_0000010">
> <DB rdf:datatype="http://www.w3.org/2001/
> XMLSchema#string">IEV_0000010</DB>
> <ID rdf:datatype="http://www.w3.org/2001/
> XMLSchema#string">Proteasome degradation</ID>
> <COMMENT rdf:datatype="http://www.w3.org/2001/
> XMLSchema#string">http://www.inoh.org (ProcessOntology)</COMMENT>
> </unificationXref>
>
> In these, I think that the DB should be something like "INOH Process
> Ontology"(or better a definitive URL for the the process ontology),
> and the ID IEV_0000010 and the comment (or better the rdfs:label)
> "Proteasome degradation"

Thanks. We will check.

> Finally, if you add something like this:
>
> <!DOCTYPE rdf:RDF [
> <!ENTITY owl "http://www.w3.org/2002/07/owl#">
> <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
> <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
> <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
> ]>
>
> at the beginning of your file between the first two lines:
>
> <?xml version="1.0" encoding="UTF-8"?>
> ************** over here *************
> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>
> you will be able to abbreviate
>
> <DB rdf:datatype="http://www.w3.org/2001/
> XMLSchema#string">IEV_0000010</DB>
>
> to
>
> <DB rdf:datatype="&xsd;string">IEV_0000010</DB>
>
> to make the file a bit shorter.