BiomaterialTermNeeds

BioMaterials Branch - Status Report - June 2007

This OBI branch deals with terms related to biomaterials. Read our status report.

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Editors

• Susanna Sansone and Melanie Courtot (Lead Editors)
• Alan Ruttenberg
• Daniel Schober
• Bjoern Peters
• Helen Parkinson
• Tina Boussard
• Philippe Rocca-Serra
• James Malone
• Alumni: Jennifer Fostel, Norman Morrison

Related Links

• Join our mailing-list

Link to conference calls

(Find here the summary of each call)

Link to OBI BioMaterial terms list

(Find here a list of excel files, as the work progresses)

List of terms submitted to the Biomaterial branch

Second round (Sept 07), terms from:

Protocol Application Branch

Redirected Terms, which were bounced from the protocol application branch.

First round (April 07), terms from:

MO

MO Transcriptomic Terms plus immuno plus Tox terms

• merged the other lists and reformatted for the conf call

contains current MO ~BioMaterial and now terms for sequences on arrays terms with definitions and mappings to PATO. Thanks to PATO (Chris M., Michael A, and George G) for the comments on the MO-PATO mappings. Terms have been added from BUG@S Bacterial array database (thanks to Adam Witney) and ~ArrayExpress. Excel file Extra columns are present in the xls file are: PATO id, PATO term, comment.

Immune Epitope

Immuno BioMaterial terms

Env

MIGS/MIMS/ICOMM BioMaterial terms

Tox

Media:Additional_terms-trxomics.xls

Proteomics

PSI BioMaterial terms

Copied by HP from call notes 27 Feb link to prexisting lists for PSI* - Proteomics/PSI sample terms are posted under OBO see MI, MOD, IPR, SEP

Polymorphism Community

-terms

Cellular Assay Community (MIACA)

terms as Excel list
and as word file, terms not related to biomaterials in grey. We are not totally sure where Materials start to be not <Bio> any more.

Perturbators.xls Examples of Media and supplements, and of perturbatortypes This is in response to the conference call on Mar 23

Flow Cytometry

Tab delimited file with terms from flow cytometry Media:Biomaterial-FlowCytometry-2007-03-30.txt

ExperiementDesign

• Tab delimited file with terms provided by Kevin Clancy:Media:clancy-exp-protocol.xls

Communities are compiling lists of their ~BioMaterial term requirements (preferably following the naming conventions^{[2| NamingConventions]}) as a tab-delimited file (term name and definition) - all needed terms if time permits. As for granularity, examples will be provided of the terms as they would be used in annotations. The term's parent class should also be specified according to an existing ontology, preferably one amongst the OBO Foundry constellation of ontologies. For example, for transcriptomics an example using terms as they exist in the MGED Ontology (MO) would be ~MaterialType as the parent class and the annotation terms of genomicDNA, cell, celllysate etc.

Lists of required relationships are also being compiled. For example, partipants are compiling relations required to create a formal specification of an action/treatment/protocol performed on a given ~BioMaterial. Where possible, candidate relations should be taken from - or at least derived from - the OBO Relations (RO) ontology.