#682 new terms requested by Bioinformatics Resource Center (BRC)

[jzheng]

Four new terms were requested by BRC for biosample annotation.

sequence assembly: A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs).

realizes some (concretizes some 'sequence assembly algorithm')
has_specified_input some 'sequence data'
has_specified_output some 'sequence data'

sequence annotation: A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data.

realizes some (concretizes some 'sequence annotation algorithm')
has_specified_output some 'sequence feature annotation'

software pipeline: A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements.

Grant Agency: An organization that provides funding support for projects such as investigations.

[jzheng]

Terms were added on Nov 27, 2013, OBI svn revision: 3905.

'sequence assembly' and 'sequence annotation' were found in software ontology (SWO).
The terms were merged in SWO from EDAM. EDMA defined terms under three branches, operations, topic, and data. They are not aligned well with BFO and IAO. Especially, the terms under topic branch are mixed BFO types. Besides, same label can be reused which is likely caused confusion. So, at this stage, we'd like to add them in OBI. We will replace the terms by SWO ones when they are well defined.

'funding organization'
http://vivoweb.org/ontology/core#FundingOrganization
with same meaning as proposed 'Grant Agency'. Since we prefer to have an OBO Foundry format ID for the term, we added it in OBI and indicated it same as vivo 'funding organization' using 'seeAlso' annotation. It might be more appropriate annotation property should be used. (Note: annotation 'xref' is not in OBI)

[Philippe Rocca-Serra]

Hi Jie, very timely wrt 'sequency assembly'

Could it be suffixed with 'process' as in 'sequence assembly process' to be able to distinguish the term from the notion of 'sequence assembly' referring to the outcome of the 'sequence assembly process' and where a 'sequence assembly' is therefore a 'sequence data'

Please see ticket:
https://sourceforge.net/p/obi/obi-terms/685/

[jzheng]

I will relabel the term as 'sequence assembly process'.

[jzheng]

Done