Specimen labeling

[obi-bot]

There is no output on the labeling process, there should be an output: labeled material.

I would propose a subclass of material labeling, specimen labeling so that we can talk about "labeled specimen" specimen labeling process: has input some material specimen has output some labeled material specimen

Reported by: jamesmalone

Original Ticket: obi/obi-terms/604

[obi-bot]

I am fine with adding 'labeled material', 'specimen labeling' and 'material labeling' if you need it. Any use cases can you provide?

So far the axioms of 'labeled specimen' look good to me.

About the definition you provided for 'specimen labeling', I don't think OBI has 'material specimen'.

Original comment by: zhengj2007

[obi-bot]

I have gone through the emails and open tickets regarding to the 'labeling process' and 'label role'

For labeling, we have the following issues being raised:

1) The labeling process should have an output. 2) The definition of label role, labeling process, and detection of label assay are interconnected in a way that causes confusion. the user has to read all three to get the overall intend. 3) The term 'label' is broader than the current definition implies.

Proposal: 1) Modify 'label role' to 'material label role', and 'labeling' to 'material labeling' (Other suggestions very welcome!), to indicate that this is not meant to cover e.g. a sticker on a tube.

2) Modify the textual definition of 'material label role' to the one pointed to by Frank in the tracker, which was agreed after a long email discussion but never put into the file. This was the proposed definition, slightly modified, followed by corresponding updated definitions:

material label role=def: a role which is borne by a material entity (me1) that is realized in an detection of label assay. The me1 acts as a proxy for another material entity (me2) and by assaying the presence or a quality of me1, the presence or a quality of me2 can be inferred.

detection of label assay=def: an assay that detects the presence or a quality of a material label which is a proxy for the detection of the labeled material entity

material labeling=def: The material addition of a labeling reagent to an input material in order to allow detection of the labeled input material

+ Add an editor note stating that all 3 definitions need to be kept in sync.

If we do this, then we can also close: http://sourceforge.net/tracker/index.php?func=detail&aid=2411372&group\_id=177891&atid=886178

3) Update logical definition to give 'material labeling' an output (James original request, concretized by Philippe)

material labeling process: has_input some material A has_input some material B and has_role some label role has_output some (material A and has_part some material B and has_role some material label role))

Note that I am proposing here that the label role is conveyed to a material at a moment it is used in a labeling process. It allows us to keep material A and B apart. I don't think we need to talk here about the disposition that material B has (fluoresence, radioactivity etc.) that enable it to be used as a label.

We should then also create labeled material=def: A processed material entity created in a material labeling process that contains a material label to allow its detection in an assay.

Logical definition: material entity and is_specified_output_of some material labeling and has_part some (has_role some material label role)

4) Update definitions of 'dye role', 'radiolabel role' and other children to reference the 'material label role' and in general be in line with the above

dye role = a material label role borne by a material that imparts color to a target material radiolabel role = a material label role borne by a material that is radioactive [radiolabel role alternative term 'label']

5) Close ancient tickets on adding 'reporter' and 'detector' roles. The present 'label role' seems to suffice for our practical needs.

Close: http://sourceforge.net/tracker/index.php?func=detail&aid=2892286&group\_id=177891&atid=886178 Close: http://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group\_id=177891&atid=886178

I am sure I have forgotten things, so constructive comments welcome. This is now added to James tracker item at http://sourceforge.net/tracker/?func=detail&aid=3410802&group\_id=177891&atid=886178

Best,

Bjoern

Original comment by: bpeters42

[obi-bot]

• priority: 7 --> 5

Original comment by: jamesmalone

[obi-bot]

Lowering priority on this so as not hold up future work. The time window when this was useful has now passed. Will fix locally and report back at future date.

Original comment by: jamesmalone

[obi-bot]

Below is as requested again the summary email with proposed changes. The only difference to the previous email is that it now incorporates the change from 'label' to 'tracer'. 'label' will be kept as an alternative term.

If you have constructive comments with concrete suggestions, please email them before next Monday. Otherwise this will be implemented at the OBI workshop in Philly as described.

- Bjoern

From: "Bjoern Peters" <bpeters@liai.org> To: "James Malone" <malone@ebi.ac.uk> Cc: "OBI Developers" <obi-devel@lists.sourceforge.net> Sent: Saturday, September 24, 2011 5:56:42 PM Subject: Re: [Obi-devel] Labeling, sampling etc

I have gone through the emails and open tickets regarding to the 'labeling process' and 'label role'

For labeling, we have the following issues being raised:

1) The labeling process should have an output. 2) The definition of label role, labeling process, and detection of label assay are interconnected in a way that causes confusion. the user has to read all three to get the overall intend. 3) The term 'label' is broader than the current definition implies.

Proposal: 1) Modify 'label role' to 'tracer role', and 'labeling' to 'adding material tracer', to indicate that this is not meant to cover e.g. a sticker on a tube.

2) Modify the textual definition of 'tracer role' to the one pointed to by Frank in the tracker, which was agreed after a long email discussion but never put into the file. This was the proposed definition, slightly modified, followed by corresponding updated definitions:

tracer role=def: a role which is borne by a material entity (me1) that is realized in an detection of label assay. The me1 acts as a proxy for another material entity (me2) and by assaying the presence or a quality of me1, the presence or a quality of me2 can be inferred.

detection of tracer assay=def: an assay that detects the presence or a quality of a tracer which is a proxy for the detection of the material entity to which the tracer is attached

adding material tracer def: The material addition of a tracer reagent to an input material in order to allow detection of the input material

+ Add an editor note stating that all 3 definitions need to be kept in sync.

If we do this, then we can also close: http://sourceforge.net/tracker/index.php?func=detail&aid=2411372&group\_id=177891&atid=886178

3) Update logical definition to give 'adding material tracer ' an output (James original request, concretized by Philippe)

adding material tracer: has_input some material A has_input some material B and has_role some tracer role has_output some (material A and has_part some material B and has_role some tracer role))

Note that I am proposing here that the tracer role is conveyed to a material at a moment it is used in a adding tracer process. It allows us to keep material A and B apart. I don't think we need to talk here about the disposition that material B has (fluoresence, radioactivity etc.) that enable it to be used as a tracer.

We should then also create tracer labeled material=def: A processed material entity created in a adding material tracer process that contains a tracer to allow its detection in an assay.

Logical definition: material entity and is_specified_output_of some adding material tracer and has_part some (has_role some tracer role)

4) Update definitions of 'dye role', 'radiolabel role' and other children to reference the 'tracer role' and in general be in line with the above

dye role = a tracer role borne by a material that imparts color to a target material radiolabel role = a tracer role borne by a material that is radioactive [radiolabel role alternative term 'label']

5) Close ancient tickets on adding 'reporter' and 'detector' roles. The present 'tracer role' seems to suffice for our practical needs.

Close: http://sourceforge.net/tracker/index.php?func=detail&aid=2892286&group\_id=177891&atid=886178 Close: http://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group\_id=177891&atid=886178

I am sure I have forgotten things, so constructive comments welcome. This is now added to James tracker item at http://sourceforge.net/tracker/?func=detail&aid=3410802&group\_id=177891&atid=886178

Best,

Bjoern

Original comment by: bpeters42

[obi-bot]

• status: open --> closed

Original comment by: mbrush

[obi-bot]

Final decisions on label/tracer related modeling were made on 4-30-12 Developer call. Documented here:

http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/developer/OBI%20Developer%20Call%20Presentations/final\_molecular\_tracer\_summary.docx?view=log

Original comment by: mbrush