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The Ontology for Biomedical Investigations
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MO request terms #568

Closed obi-bot closed 7 years ago

obi-bot commented 13 years ago

MO request some terms to be added into OBI or imported into OBI from SO or GO.

Most terms are process, few are role and study design. Please see the attached file with provided textual and logical definition.

Reported by: zhengj2007

Original Ticket: obi/obi-terms/580

obi-bot commented 13 years ago

MO request terms

Original comment by: zhengj2007

obi-bot commented 13 years ago

Some terms have been submitted before. The related tracker items are: https://sourceforge.net/tracker/?func=detail&aid=2914976&group\_id=177891&atid=886178 https://sourceforge.net/tracker/?func=detail&aid=2896768&group\_id=177891&atid=886178

Original comment by: zhengj2007

obi-bot commented 13 years ago

Discussed on Oct 18, 2010 dev call.

Four MO terms - Individual - array_manufacturer - dye_swap_quality_control - spike_quality_control have been added into OBI

Original comment by: zhengj2007

obi-bot commented 13 years ago

Updated MO request terms based on discussion

Original comment by: zhengj2007

obi-bot commented 13 years ago

Discussed on Oct 25, 2010 dev call

Following terms were agreed to be added into OBI and ID was assigned:

http://purl.obolibrary.org/obo/OBI\_0001147 label: cell culture expansion http://purl.obolibrary.org/obo/OBI\_0001149 label: gene knock in http://purl.obolibrary.org/obo/OBI\_0001148 label: gene knock out http://purl.obolibrary.org/obo/OBI\_0001150 label: chromosomal substitution http://purl.obolibrary.org/obo/OBI\_0001152 label: transfection http://purl.obolibrary.org/obo/OBI\_0001154 label: induced mutation

The following terms were added to fix some issues found during the discussion:

http://purl.obolibrary.org/obo/OBI\_0001151 label: genetically modified material http://purl.obolibrary.org/obo/OBI\_0001153 label: genetic transformation objective

Original comment by: zhengj2007

obi-bot commented 13 years ago

Following four terms discussed on Nov 8, 2010 dev call and were agreed to be added into OBI: validation by real time PCR design validation by reverse transcription PCR design validation objective reverse transcription polymerase chain reaction assay

Original comment by: zhengj2007

obi-bot commented 13 years ago

InitialTimePoint related terms were discussed on Nov 8 and 15 OBI dev calls.

The use cases of 'initialTimePoint' in MO are linked to age measurement. It is hard to model due to lake of temporal predicates. So, term 'age measurement assay' and 'age measurement datum' will be added into OBI deal with this issue. The age measurement begin with specific initial time point will be added into OBI as age measurement datum with initialTimePoint specified in the term label and only textual definition provided, such as, age since birth measurement datum. It is proposed by Bjoern on Nov 8, 2010 dev call and supported by Alan on Nov 15, 2010 dev call

Before in the MageTab file, three components indicate an age as: initialTimePoint (a process in MO) + age (a number expected) + TimeUnit (eg. year, hour, day, etc.) Now it will be replaced by OBI: age measurement datum or its subclass if the initial time point need to be specified. 'number + time unit' eg. '2 months' are expected of its instance.

Original comment by: zhengj2007

obi-bot commented 13 years ago

SO: genotype was discussed on Nov 29 dev call. Not satisfy with SO: genotype. It's a tough term and out of scope of OBI. So, decided to add "genotype information" into OBI to fit the MO use cases.

Two terms we decided to add: 1. Genetic material Textual definition: RNA or DNA deriving from immediate ancestor and part of organisms

Logical definition in OBI: (necessary conditions) (ChEBI:deoxyribonucleic acids or ChEBI:ribonucleic acids) and part_of some OBI:organism

2. genotype information Textual definition: an information content entity that is about biological sequence inheres in genetic material which is part of an organism.

Logical definition: (necessary conditions) 'IAO:information content entity' and ('is about' some SO:region and 'inheres in' some ('genetic material'and part_of some OBI:organism))

Some objections on the definition of 'genetic material' since not all genetic material come from immediate ancestor. Here are some suggested definitions: "A nucleic acid (DNA or RNA) that arises from an organism and whose variability can become manifest in properties of an organism." OR "A nucleic acid that arises from an organism, is subject to variation, and can be replicated." OR (my favorite) "A nucleic acid that arises from and can be replicated within an organism and whose variability can become manifest in properties of an organism." (proposed by Marcus Chibucos)

Original comment by: zhengj2007

obi-bot commented 12 years ago

All request terms have been added in OBI.

Original comment by: zhengj2007

obi-bot commented 12 years ago

Original comment by: zhengj2007