QuickTerm CrossProduct Examples

Let's look at an example provided by Philippe.

There are a number of terms that are need that are of the form:

• Example 1: gene expression assay using DNA microarray:

Proposed Template:

<assay> utilizes_instrument some <instrument> and has_output some information content entity about <bfo entity>

once a template has been submitted and validated, a table for submitting terms built using the template can be created as follows:

Variables are terms which may be classes and are indicates by <> in the template and may be used to define column headers in the submission table

Relations', which are indicated in bold&italic in the template, are then subsumed and do not show up in the table.

• Example 2: DNA binding site identification using DNA microarray

Relies on the previous template. The example indicates simply another OBO Foundry term source.

• Example 3: protein identification using mass spectrometry

In this last example, another template is proposed. It relies on the current definitions of Assay in OBI

Proposed Template: <OBI_instrument>, uses <reagent>, has_input <object>, has_output <GO or CHEBI>

object = OBI terms under material and any external object term we are committed to import (Chebi, cell ontology, ncbi organism taxonomy, ... ?)

General input sheet for assay quick submissions:

--> creates: 'assay that utilizes instrument <mass_spectrometer> and has_output information content entity on some <proteins>'

Same example as top above re-worked

step1: submit to the tracker the term that is missing in OBI (in this case DNA microarray, which is currently missing in OBI), [In this case, this is no longer a quick submission]

step2: instrument is now available in OBI as OBI:XXX. the devised scheme can now be used straight away as:

Again, once established, this could therefore be a totally automated submission process.