#721 assay term request

[jzheng]

Following terms are request for supporting annotation of Beta Cell Genomics studies.
DNA methylation profiling by ChIP-chip assay
epigenetic modification assay
transcription profiling by MPSS assay
histone modification identification by ChIP-chip assay
histone modification identification by ChIP-Seq assay
transcription factor binding site identification assay
transcription factor binding site identification by ChIP-chip assay
transcription factor binding site identification by ChIP-Seq assay

The attached file contains detailed definitions of the request terms.

[jzheng]

Following terms were added into OBI:
DNA methylation profiling by ChIP-chip assay
epigenetic modification assay
transcription profiling by MPSS assay
histone modification identification by ChIP-chip assay
histone modification identification by ChIP-Seq assay
transcription factor binding site identification by ChIP-chip assay
transcription factor binding site identification by ChIP-Seq assay

Notes:

1. Add equivalent axiom to the term 'transcription factor binding site identification' for classification all assays that examine transcription factor binding site under it.
2. Some of newly added terms are assays achieve specific objective. For example, ChIP-chip assay can achieve different goals, including DNA methylation, histone modification or transcription factor binding site identification. Preparation of specimen for input of assay, output information of assay and protocol used are different for achieving different goal. Current we specify all different objectives or output aboutness in ChIP-chip. When we add the terms with specific goal, the classification based on the objective does not look correct.
   Need to work out during assay harmonization.
3. Different GO terms were used for assay aboutness. For example, DNA methylation profiling assays. Some use GO:DNA methylation, some use GO:'regulation of DNA methylation'.
   Need to work out during assay harmonization

Due to the project deadline approaching, I added terms in for annotation. The terms need to be discussed.

[Alan Ruttenberg]

The definition of chip-seq assay incorrectly says that it achieves two planned objectives when it is the case that it could achieve one or the other (and possibly currently unforeseen objectives). It could be made correct (although fragile) by, instead of having axioms

achieves_planned_objective some A
achieves_planned_objective some B

use
achieves_planned_objective only (A or B)

Then have subclasses for the specific objectives (each of which should be a chip-seq assay rather than an assay which has a part which is chip-seq)

The reason the only (A or B) is fragile is because it isn't unlikely that there would be a new application of chip-seq. IMO better to leave it off and only have objectives in the subtypes.

[Alan Ruttenberg]

The assertion of participation of sonicitor only on the Chip-exo subtype seems too specific. Shouldn't it be asserted on the parent chip-seq?