Re: [Obi-devel] Labeling, sampling etc

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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 Message ----- 

> I don't think that is the case.

> You and Jie told me to remove "label" from my suggestion, so I have.
> You also said not all labeled materials are specimens so I altered my
> submission to specimen labeling as a subclass of the more generic
> material labeling and the output is a labeled specimen.

> As for roles for labeled specimen I am open to suggestion for this
> and i have therefore omitted details for this.

> Have I missed more?

> On 21/09/2011 17:47, Bjoern Peters wrote:
> > Hi James,
> 

> > It seems that you put in your original proposal, and have not
> > incorporated the feedback from Jie and myself.
> 
> > I am also doing some historic digging through the old tracker items
> > pointed out in the diverse threads, which contain additional
> > suggestions. I hope to formulate a consensus and will try to
> > summarize this by the end of the day.
> 

> > This will be for labeling stuff only for now, and I will try to
> > tackle the sample stuff tomorrow.
> 

> > - Bjoern
> 

> > ----- Original Message -----
> 

> > > Hi All,
> > 
> 

> > > Having added these tracker items, can I make these edits?
> > 
> 

> > > James
> > 
> 

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> --
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Cambridge, CB10 1SD,
> United Kingdom
> Tel: + 44 (0) 1223 494 676
> Fax: + 44 (0) 1223 494 468