Design process

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Design Decisions

Current policy is to archive design decisions in the issue tracker. [1] This is in keeping with submitting design related issues to the tracker and storing discussions there. As an example, the discussion and decision for use of input and output roles can be found in tracker item: specified ... relations - ID: 2829038. [2]

Here is wiki page to summarize design decisions that span multiple tracker items.

Use of the Unit Ontology and Unit representation within OBI

https://sourceforge.net/tracker/index.php?func=detail&aid=2896765&group_id=177891&atid=886178

Design Template discussed at the San Diego Workshop on March 2011

Service: A summary of the template discussed
http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/design_process/service.docx

Shortcut relations: An example discussed at the workshop
http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/design_process/shortcut_relations.docx

Reagent: Summary of eagle-i design presented
http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/design_process/reagent.docx

Design Template for Assays:! under construction!

OBI is designed around assays which includes processes, specifications, inputs, and outputs. An example of an assay is provided in the Quick Terms Template paper (Rocca-Serra et al., Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates, ICBO, Buffalo, NY, July, 2009). Analyte assay is taken (with some minor updating) from that paper and should be used to design other types of analyte assays but also provides a general design for other types of assays. A design template for


Analyte assays: An analyte assay is an assay with the objective to determine concentration of one substance (bearer of analyte role) that is present in (part of) another (bearer of the evaluant role). The output of the assay is information about concentration – a relational quality of the analyte towards the evaluant.

Logical definition:
(‘achieves planned objective’ some ‘analyte measurement objective’
and realizes some ('evaluant role' that ‘inheres in’ some ‘material entity’)
and realizes some ('analyte role' that ‘inheres in’ some 'scattered molecular aggregate')
and has_specified_output some ('scalar measurement datum' and ('is quality measurement of' some 'molecular concentration') and ('has measurement unit label' some concentration unit label'))

Sequencing assays: the use of a chemical or biochemical means to infer the sequence of a biomaterial

Logical definition:
(‘achieves planned objective’ some ‘assay objective’
and has_specified_input some ('ribonucleic acids' or 'deoxyribonucleic acids' or protein)
and has_specified_output some ('sequence' and is_about some quality ('primary structure of macromolecule')) and ..)