TF VIII ActionPoints 2010

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Action points (in collaboration with Juan Vizcaino, EBI)

(The main text is from J. Vizcaino formatted by M. Sharikadze. Please indicate each of your contribution with your name).

J. Vizcaino: Here you will find the list of action points we must address, in no particular order. Please, feel free to add/delete whatever you want.

Lipid nomenclature issues

submit the LipidomicNet name system to a international established database since a reference system is urgently needed.

J. Vizcaino: - We need to find out what has been already included from LIPID MAPS in the ChEBI database ( at the EBI.

J. Vizcaino: - The idea is to add the LipidomicNet lipid species names as xrefs to existing LIPID MAPS entries (about 500 lipid species would be involved).

J. Vizcaino: - It will necessary to create new lipid entries in ChEBI if not all the required lipid species are there. In total there are 853 entries from LIPID MAPS into ChEBI. I am in the process of getting the list.
For an example of an entry:

J. Vizcaino: - The list of missing entries needs to be identified first in order to estimate the amount of job involved. People from ChEBI would give us support in the process if needed.

M. Sharikadze: The link to the lipid species list M. Solleder is taking care of is placed on Wiki by S. Lehneis and is send to J. Vizcaino.

J. Vizcaino: Once I have the list from ChEBI, I will send this list to you. You will have to estimate the ones that are missing.  M. Sharikadze: The Chebi lipid list was send by J. Vizcaino, see the extract his letter To G. Schmits dated 08.02.2010.

“I got this information today from the people from ChEBI. This will be very useful in order to evaluate which lipid species are already there and which ones need to be uploaded.
The tab delimited file contains ChEBI ID, name, formula, mass, Lipid maps ids, InChI and SMILES.
The second file contains all the chemical structures where they are present in the first file.
Please, contact me if you have any question or if you think I can be of any help.”

Gene matching issues

Apparently there are genes with very interesting biological activity that cannot be matched with existing Ensembl entries at the human genome.

J. Vizcaino: - Provide a list of sequences of those genes.
J. Vizcaino: - I will study with the Ensembl people where the problems could be.
J. Vizcaino: - If necessary, we could even go to the oligo probes sequences from the array platform and match those sequences individually to the most recent assembly of the human genome.
J. Vizcaino: I don't know if similar issues happen for mouse.
M. Sharikadze: The list named “Synopsis genes and Agilent probes without EnsEMBL ID” deposited at by S. Lehneis is shared with J. Vizcaino.

Gene naming problems

There are genes for no standarized name has been decided.

J. Vizcaino: - Provide the list to me.
J. Vizcaino: - I will contact the people from the HGNC (HUGO Gene Nomenclature Committee, ) here at the EBI and get this solved.

M. Solleder: I sent a list to J. Vizcaino with the genes that I didn't find ENSEMBL-IDs for.

Organization of the meeting in Cambridge

J. Vizcaino: - I will contact the members of the WP7 in order to get feedback for the talks.
J. Vizcaino: - I will probably invite to talk people from the EBI who could be key in the solution of existing problems or future plans for the project.


J. Vizcaino: I will talk first with the members of WP7 individually and them with the leaders of the other TFs involved in the project in order to get things moving again. The idea is to be able to address the deliverables expected by month 24 of the project. I also need to evaluate what has been really done.

Access to paid databases via EBI

Is it possible to get the EBI support to access paid databases that would be interesting for the consortium?
J. Vizcaino: No idea about this. But I need a list of the potential resources you would be interested in.

Server at EBI

Check the possibility of installing servers at the EBI since the connection with Russia is very slow.

R. Noragon: the connection between University Hospital Regensburg and seems to be acceptable, measured .1 - .2 seconds. It could be that the software itself or the machine on which it is running is causing the slow response times to searches enquires.

S.Lehneis: Yes, it's definitely an application/software problem. But anyway, unfortunately for handling the synopsis list (lipid specific ontology and its gene allocations) - the BioUML webinterface only covers not really our requirements.

Doing Lipid ontology research (Synopsis list)

  • Create and visiulaize own Serverbased ontology (OBO – Open Biology Ontology) based on our synopsis list(s).
  • Do gene allocation to ontology according to the synposis list(s)
  • Allow matching: Experiment versus (parts of) Ontology
  • 4.Export matching result

S.Lehneis: Already tried AmiGO – Tools ( Unfortunately not installable locally (at least on windows system). Looking for other adequate tools or create own tools.
Searching for further similar third party tools (open source).
Otherwise create own webbased application. Writing conceptplan and timeplan is on the way.

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