[Obi-devel] Summary of developers call

[Alan Ruttenberg]

1) Paper status - Chris will send note to authors asking for consent
to send to PLOS Compbio
2) Release issues. Jie will try "export ABCL_RAM=2048" to see whether
that gets past the memory issue.
3) We discussed the relation of "primary structure of sequence
macromolecule" to SO, deciding that we would move these to be children
of generically dependent continuant and deprecate and replace with SO
terms once we were clear on what the replacements should be. We
defined 'sequence data' to be measurement data that is about primary
structure of sequence macromolecule, and used the new term in sequence
assay. Will check in as soon as classification finishes successfully.
4) Reviewed 9 devices from spreadsheet. There were sufficient comments
that it seems this is a worthwhile exercise to continue. Carlo will
follow up on the comments that were made

-Alan

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[Jie Zheng]

Hi Alan,

I tried to increase the memory using "export ABCL_RAM=2048". It still
failed in generating 'inferred-superclasses.owl'. Main issue is
"java.lang.OutOfMemoryError: Java heap space".

I attach a compressed file that contains the output message of running
the script (Infer-mesg.txt), the bash file I ran
(OBIrelease-8-infer-0628), and the files that generated during release
process. The OBI files revision 2974 were used. Could you please have a
look? If you need, you can login to my account to check it.

Thanks,

Jie

[Alan Ruttenberg]

Hi Jie,

I had a look at this today in Protege 4. To do so I did the following:

1) Copy the external directory from the trunk into the release
directory (the one in the zip isn't complete)
2) Copy the file catalog-v001.xml from the branches directory into the
newids folder.
3) Open obi.owl
4) Manually import the files disjoints.owl and assumed-individuals.owl
5) Classify using Hermit.

In doing so I see a number of unsatisfiable classes. I don't have time
to debug what the problem is now. I can try to do so but will be away
for a week with limited internet access.

I'm attaching a snapshot of the unsat classes in case it gives a hint
to someone else of what the problem is. Recall that as we add
disjoints in the build, classes that might have been satisfiable
before might only be caught as unsatisfiable once the disjoints are
added.

-Alan

[Jie Zheng]

Hi Alan,

Thanks for looking at it. I will try the way you are doing to see
whether reasoning works and look details of unsatisfied classes.

Jie

>> ------------------------------------------------------------------------

[Jie Zheng]

Hi All,

I manually imported disjoints.owl and assumed-individuals.owl into
obi.owl using both Protege 3.4.4 and Protege 4.1. I got exactly
inconsistent classes as Alan got when reasoning with Hermit in Protege
4.1. By using Pellet Protege 3.4.4, I got the same inconsistent classes
as those indicated by Hermit and ran into out of memory issue. Without
importing disjoints.owl, reasoning is fine.

Most of inconsistent classes are chromatography related terms. There are
many disjoint classes associated with them. I have no idea which one
cause the problem. I will appreciate it very much if anyone would like
to help on it. I have attached disjoints.owl and
assumed-individuals.owl. Open the obi.owl using Protege 4.1 and then
import the attached owl files. After reasoning using Hermit, you can see
the inconsistent classes.

Thanks,

Jie

>> ------------------------------------------------------------------------
>>

[Philippe Rocca-Serra]

Hi Everyone,

I have been trying to import several classes from RNAO and modified my
local copies of external.owl and externalDerived.owl as follows:

i. external.owl

addition of RNAO namespace:
xmlns:rnao="http://purl.org/obo/owl/RNAO#"

and then

<owl:Class rdf:about="http://purl.org/obo/owl/RNAO#RNAO_0000173">
<rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
<IAO_0000412 rdf:resource="http://purl.org/obo/owl/RNAO"/>
</owl:Class>

ii. externalDerived.owl

addition of RNAO namespace:
xmlns:rnao="http://purl.org/obo/owl/RNAO#"

and then

<!-- purine N7 atom-->
<rdf:Description rdf:about="http://purl.org/obo/owl/RNAO#RNAO_0000173">
<rdfs:label xml:lang="en">purine N7 atom</rdfs:label>
<obi:IAO_0000111 xml:lang="en">purine N7 atom</obi:IAO_0000111>
</rdf:Description>

Opening obi-edit.pprj shows the RNAO class but I can not get it to
locate as a subclass of Material Entity (note this is just a test, it
did not work either when I tried to subclass it as molecular entity from
CHEBI

The Purl for RNAO seems to be valid. Any clue as to what could cause the
fault?

Thanks for your help

Philippe

[Jie Zheng]

Hi Philippe,

The 'purine N7 atom' is imported under material_entity after I modified
external.owl and externalDerived.owl as you said. Please see the
attached files.

As you mentioned, it is more appropriate to import it under 'molecular
entity'.

Best,

Jie

> ------------------------------------------------------------------------
>

[Philippe Rocca-Serra]

Hi Jie,

thanks for checking on this. It works with your file but not mine. How
rude ! :)

I have run a diff between your file and mine and can not spot anything
major except the "owl:Ontology rdf:about="" but even changing it in my
case does not fix the import.
which leaves the order but then again, does not make much sense....

Arghh!! just found the b...dy typo at the beginning

diff external.owl external-old.owl <!-- this means diff jie's file
philippe's file
1c1
< <?xml version="1.0"?>
---
> d<?xml version="1.0"?>
17c17

thanks again.

--
/-----------------------------------------------\
Philippe Rocca-Serra (PhD)
EMBL-EBI
NET-Project Technical Coordinator
Tel: +44 (0)1223 492553
Fax: +44 (0)1223 494
URL:
http://www.ebi.ac.uk/net-project/
http://isatab.sourceforge.net/index.html
\-----------------------------------------------/

[Jie Zheng]

Hi Philippe,

You are welcome.

Since it is typo, it means you can miroet as many terms as you want by
yourself in the future. :-)

However, I will add RNAO to the template file for generating
externalDerived.owl scripts. Otherwise, when we run the script to update
externalDerived.owl, all the information you added manually will be
missing. When I am done, I will let you know and you can follow the
tutorial on the OBI wikipage to run the script to generate
externalDerived.owl. It is easy and the program is platform independent.

Best,

Jie