[Obi-instrument-branch] next instrument call (6. May 2008) - agenda

[Daniel Schober]

Hello all,
We have a call tomorrow (see agenda below). Any further ideas? 
Please add where needed on the wiki at
https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

13. May 2008

Agenda:

• Check new Branch Report items
• Review status of Function/PA discussions, i.e. do we agree on:
  • "As the issue of function later came up with the instrument branch, Bjoern and Bill recommended they work with the PA branch to see that all the required 'minimal PAs' linked to a specific function are created and then can be linked to the appropriate instrument using the 'has_minimal_PA' relation. I've agreed to help the instrument branch review their current spreadsheet and guarantee the needed 'minimal PAs' exist or are submitted to the PA branch for creation. These will later be converted to bfo:functions algorithmicaly at which point a more complete, formal representation of all the pieces - including those needed for R2 & R3 - can be implemented."
• Add missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
• decide on next steps

Best,
    Daniel Schober.

Daniel Schober wrote:

-- 
__________________________________________________________________________________________

Dr. Daniel Schober

NET Project - Ontologist

The European Bioinformatics Institute   email:  sch...@ebi.ac.uk
EMBL Outstation - Hinxton               direct: +44 (0)1223 494410
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                 	Room: A3-141 (extension building)

Project page: www.ebi.ac.uk/net-project

Personal page:    http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/

[Daniel Schober]

Additionally to the agenda send out yesterday (below, sorry for the erroneous date in subject line) we might also add some new terms provided by Phillippe (see xls attached) to the instruments file.
Cheers, Daniel.

Daniel Schober wrote:

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[Daniel Schober]

Hello all,
We have a call tomorrow (see agenda below). Any further ideas?
Please add where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

  Agenda for 20. May 2008:
* Review status of Function/PA discussions,
* Continue to add last missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
* decide on next steps

Best,
    Daniel Schober.

[frank gibson]

Hi,

I am not sure if I will be able to make the call today, I will try,
but it is unlikely, sorry for the short notice.

Frank

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Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
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[Daniel Schober]

Hello all,
Given that Frank is not there today and that we are still working on the way the has_function range should be modeled, we might skip todays instrument call, but we'll see who else is available.
I assume a possible action item for the next call will be to evaluate the use case Philippe and me have provided and then add/implement all needed RUs tackling our instrument-branch. Any further ideas?

Please add where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

  Possible agenda for 27. May 2008:
* Continue to add last missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en

* decide on next steps

     (e.g. implement device classes as needed by use case at http://docs.google.com/Doc?docid=dg9kgrmp_1hjv9jnf6&hl=en)

Best,
    Daniel Schober.

[Daniel Schober]

Hello all,

We have an instrument call today at 4 pm BST. Please add to the proposed agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 03. June 2008:

* Prepare branch report as requested on cc list (26/05/2008 23:53)
 ** Collect issues, draft report outline according to our last report and check if what we do is in harmony with what others do (avoid redundancy)
* Evaluate the use case Philippe and me have provided and then add/implement all needed RUs tackling our instrument-branch.
* Continue to add last missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
* implement device classes as needed by use case at http://docs.google.com/Doc?docid=dg9kgrmp_1hjv9jnf6&hl=en
* next steps and term submissions (e.g. from Philippe, terms form PSI MS, MSI NMR, ...) ?

Best,
    Daniel Schober.

[Daniel Schober]

Hello all,

We have an instrument call tomorrow at 4 pm BST. Please have a look at the initial structure for our branch report and add what you feel is missing: http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en
Please also add to the proposed agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 10. June 2008:

* Prepare branch report as requested on cc list (26/05/2008 23:53) and review http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en
 **check if what we do is in harmony with what others do (avoid redundancy)
if time permits:

* Evaluate the use case Philippe and me have provided and then add/implement all needed RUs tackling our instrument-branch.

* Implement device classes as needed by use case at http://docs.google.com/Doc?docid=dg9kgrmp_1hjv9jnf6&hl=en
* Continue to add last missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
* Next steps and term submissions (e.g. from Philippe, terms form PSI MS, MSI NMR, ...) ?

Best,
    Daniel Schober.

[Daniel Schober]

Hello all,

We have an instrument call tomorrow at 4 pm BST. Please have a second look at our branch report and add what you feel is missing: http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en
Please also add to the proposed agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 17. June 2008:
* Prepare branch report as requested on cc list (26/05/2008 23:53) at  http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en
  if time permits:

* Implement device classes as needed by use case at http://docs.google.com/Doc?docid=dg9kgrmp_1hjv9jnf6&hl=en

* Continue to add last missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en

Best,
    Daniel Schober.

[frank gibson]

Hi Daniel,

Apologies for the short notice, unfortunately I will be unable to
attend the call today. However I have been through the document and
other than my previous comments highlighted in the document, it looks
fine

Cheers

Frank

On Mon, Jun 16, 2008 at 1:37 PM, Daniel Schober <sch...@ebi.ac.uk> wrote:
> Hello all,
>
> We have an instrument call tomorrow at 4 pm BST. Please have a second look
> at our branch report and add what you feel is missing:
> http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en

> Please also add to the proposed agenda where needed on the wiki at
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls
>

> Agenda for 17. June 2008:
> * Prepare branch report as requested on cc list (26/05/2008 23:53) at
> http://docs.google.com/Doc?docid=dg9kgrmp_2f447dkgf&hl=en
> if time permits:
> * Implement device classes as needed by use case at
> http://docs.google.com/Doc?docid=dg9kgrmp_1hjv9jnf6&hl=en

> * Continue to add last missing definitions for device functions on
> http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
>
> Best,
> Daniel Schober.

>
> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>
>

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--
Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
Newcastle upon Tyne, NE1 7RU
United Kingdom
Telephone: +44-191-246-4933
Fax: +44-191-246-4905

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[Daniel Schober]

Hello all,
I have just published our report, but it still needs some finalization (e.g. link to the instrument function google doc, ...). Please have a go.
I can' t make it to next weeks call, so please feel free to initiate one yourself.
Agenda can be put on 

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Best,
    Daniel Schober.

[Melanie Courtot]

Hi all,

We have two instrument calls left before the workshop, Daniel is away next
week and I will be the following one.

1. 24th June
DS away

2. 1st July
MC away

Could you let us know if you plan to attend any of those calls?

Thanks,
Melanie

> Hello all,
> I have just published our report, but it still needs some finalization
> (e.g. link to the instrument function google doc, ...). Please have a go.
> I can' t make it to next weeks call, so please feel free to initiate one
> yourself.
> Agenda can be put on
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls
>

> **

> Best,
> Daniel Schober.
>
> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>

[Melanie Courtot]

Hi,

Tomorrow's instrument call is now canceled and I updated the OBI calendar.
Last chance to let us know if you will attend next week :-)

Thanks,
Melanie

[Daniel Schober]

Hello all,
Frank wants to/has added the functions and their metadata from the google spreadsheet  to the owl file, so today we can start experimenting with these.
I think on the OBI WS we said we wanted to concentrate on the use cases, but we can wave a call today to do the functions (many needed for the use cases anyway).
What do others think?
Please add to the agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

  Agenda for 15. July 2008:
* Use case discussions ?
Review status of Function, finalize their metadata (possibly within the owl file?).
* Continue to add last missing functions definitions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
* decide on next steps


Best,
    Daniel Schober.

[Daniel Schober]

Hello all,
We can have a call today and I think we should concentrate on Richards use case (see below).

Please add to the agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 22. July 2008

* Look at Richard Scheuermann's use case at  
        https://wiki.cbil.upenn.edu/obiwiki/index.php/EvaluationPhase1Submissions#
* Start listing device related requirements (and add to xls sheet or owl file ?)

Best,
    Daniel Schober.



---

From Richard Scheuermann, Jan 2008

1. We wish to annotate an experiment performed as part of an investigation in which the effects of a particular amino acid substitution in the PB1-F2 protein of influenza virus is being evaluated. Although the investigators consider the experiment in question to be one experiment, several discrete steps of sample processing, assaying and data analysis are involved as listed below. We would like to annotate the experiment in such a way as to allow the ability to recognize other experiments that use some of the same sub-process steps.

• a. Generation of recombinant viruses using reverse genetic approaches in which recombinant plasmids are transfected into cells to produce recombinant viruses.
• b. Generation of mutant recombinant plasmids using site-directed mutagenesis.
• c. Infection of mice using recombinant viruses.
• d. Preparation of a homogenate specimen from the lungs of infected mice.
• e. Measurement of interferon gamma levels in the lung homogenate specimen by ELISA.
• f. Measurement of influenza virus titers in the lung homogenate specimen by plaque assay.
• g. Conversion of the primary ELISA data as measured by light absorbance into interferon gamma amounts by standard curve interpolation.
• h. Conversion of interferon gamma amount into interferon gamma concentration with a simple algebraic equation.
• i. Comparison of interferon gamma concentrations in lung homogenates derived from mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different using a students t test.
• j. Conversion of virus titers at different time following infection in lung homogenates derived from mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different using a students t test.
• k. Comparison of Kaplan-Meier survival curves for mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different.

https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:OBI_Use_Case.xls

https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:Conenello_2007_PB1-F2.pdf

2. We wish to build a database that can capture descriptions of a wide variety of different experiments being performed by investigators interested in immunology and infectious diseases such that database users have the ability to identify experiments that share user-selected common features and extract selected data derived from those experiments. The common experiment features would include:

• a. a common assay (e.g. flow cytometry)
• b. a common type of assay (e.g. all assays in which protein levels are measured)
• c. a common treatment condition (e.g. anthrax vaccine)
• d. a common analyte evaluated (e.g. interleukin 2)
• e. a common type of analyte evaluated (e.g. cytokines)
• f. a common experiment type (e.g. survival experiments)
• g. a common conditional variable (e.g. type 1 diabetes)
• h. a common type of conditional variable (e.g. autoimmune disease)

3. Gene Ontology annotation has proved to be a useful way of describing the function of proteins in such a way as to allow for the inference of protein relationships to be inferred through the structure of the ontology used to annotate the proteins. We would like to develop a complementary system for describing protein relationships based on data derived from two types of biological networks, protein-protein interaction networks and gene expression correlation networks (sometimes called by the misnomer genetic interaction networks). Different methods have been developed to describe the topological properties of these networks. Some of the properties are related to the nodes or vertices of the graph (proteins or genes), some are related to the edges of the graph (interactions or correlations), some are related to the entire network as a whole, and some are related to sub-graphs (modules) within the network. Since the values of these properties are dependent on the methods used, we would like to be able to annotate each of the network components with property values and the methodological details related to the property values. Some of the properties include:

• a. For nodes - connectivity, module membership
• b. For edges - betweenness, weight
• c. For networks - average connectivity, average betweenness, other distributional characteristics of these properties, size
• d. For sub-graph modules - node membership, edge membership, density

[Melanie Courtot]

Hi Daniel,
I am at the ISMB (as is Frank) and I won't be able to attend the call.
Thanks,
Melanie

> Hello all,
> We can have a call today and I think we should concentrate on Richards
> use case (see below).
>
> Please add to the agenda where needed on the wiki at
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls
>

> *Agenda for 22. July 2008*

>
> * Look at Richard Scheuermann's use case at
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/EvaluationPhase1Submissions#
> * Start listing device related requirements (and add to xls sheet or owl
> file ?)
>
> Best,
> Daniel Schober.
>
>
>
> ---
>

> *From Richard Scheuermann, Jan 2008*

>
> 1. We wish to annotate an experiment performed as part of an
> investigation in which the effects of a particular amino acid
> substitution in the PB1-F2 protein of influenza virus is being
> evaluated. Although the investigators consider the experiment in
> question to be one experiment, several discrete steps of sample
> processing, assaying and data analysis are involved as listed below. We
> would like to annotate the experiment in such a way as to allow the
> ability to recognize other experiments that use some of the same
> sub-process steps.
>

> * a. Generation of recombinant viruses using reverse genetic

> approaches in which recombinant plasmids are transfected into
> cells to produce recombinant viruses.

> * b. Generation of mutant recombinant plasmids using site-directed
> mutagenesis.
> * c. Infection of mice using recombinant viruses.
> * d. Preparation of a homogenate specimen from the lungs of infected
> mice.
> * e. Measurement of interferon gamma levels in the lung homogenate
> specimen by ELISA.
> * f. Measurement of influenza virus titers in the lung homogenate
> specimen by plaque assay.
> * g. Conversion of the primary ELISA data as measured by light

> absorbance into interferon gamma amounts by standard curve
> interpolation.

> * h. Conversion of interferon gamma amount into interferon gamma

> concentration with a simple algebraic equation.

> * i. Comparison of interferon gamma concentrations in lung

> homogenates derived from mice infected with two types of viruses
> that differ at a single amino acid position of the PB1-F2 protein
> to determine if they are statistically different using a students
> t test.

> * j. Conversion of virus titers at different time following

> infection in lung homogenates derived from mice infected with two
> types of viruses that differ at a single amino acid position of
> the PB1-F2 protein to determine if they are statistically
> different using a students t test.

> * k. Comparison of Kaplan-Meier survival curves for mice infected

> with two types of viruses that differ at a single amino acid
> position of the PB1-F2 protein to determine if they are
> statistically different.
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:OBI_Use_Case.xls
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:Conenello_2007_PB1-F2.pdf
>
>
> 2. We wish to build a database that can capture descriptions of a wide
> variety of different experiments being performed by investigators
> interested in immunology and infectious diseases such that database
> users have the ability to identify experiments that share user-selected
> common features and extract selected data derived from those
> experiments. The common experiment features would include:
>

> * a. a common assay (e.g. flow cytometry)
> * b. a common type of assay (e.g. all assays in which protein levels
> are measured)
> * c. a common treatment condition (e.g. anthrax vaccine)
> * d. a common analyte evaluated (e.g. interleukin 2)
> * e. a common type of analyte evaluated (e.g. cytokines)
> * f. a common experiment type (e.g. survival experiments)
> * g. a common conditional variable (e.g. type 1 diabetes)
> * h. a common type of conditional variable (e.g. autoimmune disease)

>
> 3. Gene Ontology annotation has proved to be a useful way of describing
> the function of proteins in such a way as to allow for the inference of
> protein relationships to be inferred through the structure of the
> ontology used to annotate the proteins. We would like to develop a
> complementary system for describing protein relationships based on data
> derived from two types of biological networks, protein-protein
> interaction networks and gene expression correlation networks (sometimes
> called by the misnomer genetic interaction networks). Different methods
> have been developed to describe the topological properties of these
> networks. Some of the properties are related to the nodes or vertices of
> the graph (proteins or genes), some are related to the edges of the
> graph (interactions or correlations), some are related to the entire
> network as a whole, and some are related to sub-graphs (modules) within
> the network. Since the values of these properties are dependent on the
> methods used, we would like to be able to annotate each of the network
> components with property values and the methodological details related
> to the property values. Some of the properties include:
>

> * a. For nodes - connectivity, module membership
> * b. For edges - betweenness, weight
> * c. For networks - average connectivity, average betweenness, other

> distributional characteristics of these properties, size

> * d. For sub-graph modules - node membership, edge membership, density

>
>
> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>

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[Daniel Schober]

Hi Instrumenteers,
Because many participants are at ISMB, todays instrument call is cancelled.
Cheers,
 Daniel Schober.

[Daniel Schober]

Hello all,
We have a call tomorrow and I think we should concentrate on Richards use case (see below).

Please add to the agenda where needed on the wiki at

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 29. July 2008

* Look at Richard Scheuermann's use case at  
        https://wiki.cbil.upenn.edu/obiwiki/index.php/EvaluationPhase1Submissions#
* Start listing device related requirements (and add to xls sheet or owl file ?)

Best,
    Daniel Schober.



---

From Richard Scheuermann, Jan 2008

1. We wish to annotate an experiment performed as part of an investigation in which the effects of a particular amino acid substitution in the PB1-F2 protein of influenza virus is being evaluated. Although the investigators consider the experiment in question to be one experiment, several discrete steps of sample processing, assaying and data analysis are involved as listed below. We would like to annotate the experiment in such a way as to allow the ability to recognize other experiments that use some of the same sub-process steps.

• a. Generation of recombinant viruses using reverse genetic approaches in which recombinant plasmids are transfected into cells to produce recombinant viruses.

• b. Generation of mutant recombinant plasmids using site-directed mutagenesis.

• c. Infection of mice using recombinant viruses.

• d. Preparation of a homogenate specimen from the lungs of infected mice.

• e. Measurement of interferon gamma levels in the lung homogenate specimen by ELISA.

• f. Measurement of influenza virus titers in the lung homogenate specimen by plaque assay.

• g. Conversion of the primary ELISA data as measured by light absorbance into interferon gamma amounts by standard curve interpolation.

• h. Conversion of interferon gamma amount into interferon gamma concentration with a simple algebraic equation.

• i. Comparison of interferon gamma concentrations in lung homogenates derived from mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different using a students t test.

• j. Conversion of virus titers at different time following infection in lung homogenates derived from mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different using a students t test.

• k. Comparison of Kaplan-Meier survival curves for mice infected with two types of viruses that differ at a single amino acid position of the PB1-F2 protein to determine if they are statistically different.

https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:OBI_Use_Case.xls

https://wiki.cbil.upenn.edu/obiwiki/index.php/Image:Conenello_2007_PB1-F2.pdf

2. We wish to build a database that can capture descriptions of a wide variety of different experiments being performed by investigators interested in immunology and infectious diseases such that database users have the ability to identify experiments that share user-selected common features and extract selected data derived from those experiments. The common experiment features would include:

• a. a common assay (e.g. flow cytometry)

• b. a common type of assay (e.g. all assays in which protein levels are measured)

• c. a common treatment condition (e.g. anthrax vaccine)

• d. a common analyte evaluated (e.g. interleukin 2)

• e. a common type of analyte evaluated (e.g. cytokines)

• f. a common experiment type (e.g. survival experiments)

• g. a common conditional variable (e.g. type 1 diabetes)

• h. a common type of conditional variable (e.g. autoimmune disease)

3. Gene Ontology annotation has proved to be a useful way of describing the function of proteins in such a way as to allow for the inference of protein relationships to be inferred through the structure of the ontology used to annotate the proteins. We would like to develop a complementary system for describing protein relationships based on data derived from two types of biological networks, protein-protein interaction networks and gene expression correlation networks (sometimes called by the misnomer genetic interaction networks). Different methods have been developed to describe the topological properties of these networks. Some of the properties are related to the nodes or vertices of the graph (proteins or genes), some are related to the edges of the graph (interactions or correlations), some are related to the entire network as a whole, and some are related to sub-graphs (modules) within the network. Since the values of these properties are dependent on the methods used, we would like to be able to annotate each of the network components with property values and the methodological details related to the property values. Some of the properties include:

• a. For nodes - connectivity, module membership

• b. For edges - betweenness, weight

• c. For networks - average connectivity, average betweenness, other distributional characteristics of these properties, size

• d. For sub-graph modules - node membership, edge membership, density

[frank gibson]

Hi Daniel,

I have been through the use-case and I have failed to see any mention
of any device. Have you seen any? This use-case is going to be
difficult to do because in general it is not very explicit in its
description of anything. I don't want to play detective and try and
guess what devices were used with what settings. They need to be
explicitly stated. If this is the only agenda item I would favor not
having the call and stating this at the call on Wednesday. What is
your feeling on this?

Frank

On Mon, Jul 28, 2008 at 5:00 PM, Daniel Schober <sch...@ebi.ac.uk> wrote:
> Hello all,

> We have a call tomorrow and I think we should concentrate on Richards use
> case (see below).
>

> Please add to the agenda where needed on the wiki at
>
> https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls
>

> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>
>

> -------------------------------------------------------------------------
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--

Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
Newcastle upon Tyne, NE1 7RU
United Kingdom
Telephone: +44-191-246-4933
Fax: +44-191-246-4905

-------------------------------------------------------------------------

[Daniel Schober]

Hi instrumenteers,

Yes Frank, I have noticed this too. The use case xls does not mention instruments specificly, and only references them implicitly. The xls concentrates on protocols and its inputs and outputs.
However some devices are mentioned in the pdf  Materials & Methods section, e.g. for 'Constructs and Cloning':
reverse transcription kit
RNA extraction kit
PCR cycler
Stratagene Quick-Change mutagenesis kit (Stratagene, http://www.stratagene.com/)
DNA Sequencer (at Mount Sinai sequencing core facility)
...
But some are referenced rather unspecificly and general, and sometimes methods are just xrefs to external papers.
I am however not sure if this should make us reject this use case. If they are not exaustive in this area, maybe they do not think capturing more is usefull for their purpose. We should ask them on this issue, but  I think with any use case there will be some disadvantage for this or that branch. Besides this is just the first. I estimate that we need at least 2-3 use cases. So my feeling would be to just start with this one and model its occuring devices on the general (be it function or process or protocoll -derived ) level.
 What do you think?
Cheers, Daniel.

[frank gibson]

Hi Daniel,

Comments in line

On Tue, Jul 29, 2008 at 9:56 AM, Daniel Schober <sch...@ebi.ac.uk> wrote:
> Hi instrumenteers,
>
> Yes Frank, I have noticed this too. The use case xls does not mention
> instruments specificly, and only references them implicitly. The xls
> concentrates on protocols and its inputs and outputs.
> However some devices are mentioned in the pdf Materials & Methods section,
> e.g. for 'Constructs and Cloning':
> reverse transcription kit

This is a chemical kit

> RNA extraction kit

This is a chemical kit

This is a chemical kit
> PCR cycler

Yes, this is a device

> Stratagene Quick-Change mutagenesis kit (Stratagene,
> http://www.stratagene.com/)

This is a chemical kit

> DNA Sequencer (at Mount Sinai sequencing core facility)

This is a device, However it gives the implication it was done of site
so they probably have limited knowledge of how it was used

> ...
> But some are referenced rather unspecificly and general, and sometimes
> methods are just xrefs to external papers.

This is a failing of the description of the case study

> I am however not sure if this should make us reject this use case.

No, we just need more detail

If they
> are not exaustive in this area, maybe they do not think capturing more is
> usefull for their purpose.

That is a fair point

We should ask them on this issue, but I think
> with any use case there will be some disadvantage for this or that branch.

I would agree

> Besides this is just the first. I estimate that we need at least 2-3 use
> cases.

Absolutely

So my feeling would be to just start with this one and model its
> occuring devices on the general (be it function or process or protocoll
> -derived ) level.

Absolutely. My concern is that I don't want to guess what they did. If
they use a device then they must tell us, then we can do something
about it

I think we have clear questions for the developers call tomorrow. Do
you think there is a need for a call this afternoon?

Frank

> What do you think?
> Cheers, Daniel.
>
>
>
> frank gibson wrote:
>

[Daniel Schober]

Hi,
Kits are on the border to Chemicals / materials  They could be made a device sibling or subclass in any case they are under material entity.
e.g. a defined class: material entity that has_part chemical compound and has_part simple device (and has_part  consumable) or something like this.

O.k. lets skip the call today and lets voice our concerns regarding device-blur in this use case at the call tomorrow.

[Alan Ruttenberg]

I think sibling. Collection of reagents, devices, protocols.

-Alan

[frank gibson]

On Tue, Jul 29, 2008 at 2:15 PM, Alan Ruttenberg
<alanrut...@gmail.com> wrote:
> I think sibling. Collection of reagents, devices, protocols.

Yes, they are presented as a collection for a specific purpose
(objective or whatever). Hopefully we will get some concrete examples
as a result of the case study

Frank

> -Alan
> On Jul 29, 2008, at 7:47 AM, Daniel Schober wrote:
>

--

Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
Newcastle upon Tyne, NE1 7RU
United Kingdom
Telephone: +44-191-246-4933
Fax: +44-191-246-4905

-------------------------------------------------------------------------

[Daniel Schober]

Hello all,
There will be no instrument call today, as we still concentrate on the OBI use case (which is sparse on instruments). I am however preparing the nmr terms and Chrom CV terms for submission into OBI. Expect to receive the next round term lists in xls format next month.

[Daniel Schober]

Hello all,
We might still skip the instrument call, as we still concentrate on the OBI use case.
 I am still preparing the nmr and Chrom CV terms for submission into OBI.
Alternatively we could discuss this on a call today. Any other agenda items? What do you think?

Are we all happy with a submission in the following format ?

class (ID)
label
URI
parent_class (ID), current
parent_label, current
parent_URI, current
OBI_0000275 (editor note)
Existing obi parent class, new
Non existing (recommended) OBI parent class, new
Obi merge note (refactoring recommendation)
OBI_0000291 definition
OBI_0000286 alternative name
OBI_0000279 definition source
OBI_0000274 definition editor
OBI_0000288 preferred name
OBI_0000281 curation status

This can be easily imported by Jason Greenbaums table importer tool (which works now).
Best,
    Daniel Schober.

[frank gibson]

Hi Daniel,

The format looks fine, without testing it out. I would postpone the
call today in favour of the use-case calls this week.

Thanks

Frank

> --
> __________________________________________________________________________________________
>
> Dr. Daniel Schober
>
> NET Project - Ontologist
>
> The European Bioinformatics Institute email: sch...@ebi.ac.uk
> EMBL Outstation - Hinxton direct: +44 (0)1223 494410
> Wellcome Trust Genome Campus fax: +44 (0)1223 494 468
> Cambridge CB10 1SD, UK Room: A3-141 (extension building)
>
> Project page: www.ebi.ac.uk/net-project
>
> Personal page:
> http://www.ebi.ac.uk/Information/Staff/person_maint.php?s_person_id=734
> Former home page: http://www.bioinf.mdc-berlin.de/%7Eschober/
>
>

> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Obi-instrument-branch mailing list
> Obi-instru...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>

--

Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,
Newcastle upon Tyne, NE1 7RU
United Kingdom
Telephone: +44-191-246-4933
Fax: +44-191-246-4905

https://homepages.cs.ncl.ac.uk/frank.gibson

[Daniel Schober]

Yes, lets get these use cases up and running first.
--> No call today.

Cheers, Daniel.

frank gibson wrote:

[Daniel Schober]

Hello all,
Due to lots of people traveling (MGED meeting or summer vacation) there
will be no instrument call today.

[Daniel Schober]

Hello all,
Should we pause the instrument calls until we proceed with obi and its
use cases? When we have one done, its devices need to be put in the
instruments file, or instrument related issues arise, we can have calls
again. So in short my suggestion is to have instrument calls on a
per-issue basis rather than weekly for the moment.
I think that is what other branches do as well.
What do you think ?

[Allyson Lister]

we could do that, or we could make the instrument calls part of the use-case calls?

:)

2008/9/9 Daniel Schober <sch...@ebi.ac.uk>

--
Thanks,
Allyson :)

Allyson Lister
Research Associate
Centre for Integrated Systems Biology for Ageing and Nutrition
Newcastle University
http://www.cisban.ac.uk
School of Computing Science
Newcastle University

[Ryan Brinkman]

Works for me as 8am is difficult.

[Daniel Schober]

Hello all,
We agreed to resume the instrument calls from tomorrow on.

Please add to the agenda where needed on 

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 14. October 2008:

• Branch clean up (e.g. addressed editor notes)
• Work out how to do a device mini use case "flow cytometer used to count CD8 positive cells" (e.g. http://www.scq.ubc.ca/flow-cytometry-a-technology-to-count-and-sort-cells/)
  • Pick a most important relations between instrument, manufacturer, function, protocol application, Biomaterial/sample, device part, instrument parameter, software and protocol and try to model.
• Next round term submissions (nmr and Chrom CV terms) via xl2owl tool (http://70.167.3.46/~jgbaum/cgi-bin/xl2owl.cgi)

Best,
    Daniel Schober.

[Daniel Schober]

Hello all,
We have an instrument branch call tomorrow

Please add to the agenda where needed on 

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda:

• Clean file according to http://ashby.csail.mit.edu/web/2008/obi/reports/InstrumentAndPart_report.html
• Update device relations list at https://wiki.cbil.upenn.edu/obiwiki/index.php/ListOfRelationships
• Binning under defined classes Policy discussion
• Discuss Differrentiae of 'instrument': has_parameter_set
  

• Work out how to do a device mini use case "flow cytometer used to count CD8 positive cells" (e.g. http://www.scq.ubc.ca/flow-cytometry-a-technology-to-count-and-sort-cells/)
  • Pick a most important relations between instrument, manufacturer, function, protocol application, Biomaterial/sample, device part, instrument parameter, software and protocol and try to model.

[Melanie Courtot]

Hi all,

Just a few comments on the agenda:

- binning under defined classes: I thought the decision/discussion already happened. In any case if we feel there is an issue the Instrument branch probably won't be able to take any decision. So I would propose to move this to a dev agenda if needed.

There is a wiki page stating the current policy at https://wiki.cbil.upenn.edu/obiwiki/index.php/DefinedClasses

- for the mini use case I think working out the manufacturer relation should be pretty straightforward and would be helpful for the biomaterial branch as well, so that would be my pick :)

Thanks,

Melanie

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---

Mélanie Courtot

TFL- BCCRC

675 West 10th Avenue

Vancouver, BC

V5Z 1L3, Canada

[Ryan Brinkman]

Sorry I need the car tomorrow for a later meeting , but that means I need to bring the kids into daycare at  8am, which means I can’t make the call.

 

Regrets,

Ryan

[frank gibson]

agree with Melanie, decsion has been made. You need to bring it up on
the dev call or for the F2F

Cheers

Frank

> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/obi-instrument-branch
>
>

--

Frank Gibson
Research Associate
Room 2.19, Devonshire Building
School of Computing Science,
Newcastle University,

Newcastle upon Tyne, NE1 7RU

United Kingdom
Telephone: +44-191-246-4933
Fax: +44-191-246-4905
https://homepages.cs.ncl.ac.uk/frank.gibson

-------------------------------------------------------------------------

[Daniel Schober]

Hello all,
Please excuse me for not attending the last call. I was sick at home the last days and couldn't reach anyone to inform you either, because I don't have internet and Susanna and Phillippe were away. We can have an instrument branch call next week.

Please add to the agenda where needed on 

https://wiki.cbil.upenn.edu/obiwiki/index.php/InstrumentTermCalls#Summary_of_the_Instrument_Branch_Conference_Calls 

Agenda for 2nd. December 2008

• The possible inclusion of consumes data, produces data as functions. For example, the device was designed with the intent to produce data.

-consume_data: Is a function that in borne by in a material entity by virtue of its structure. When realized the material entity consumes (has an input of) data.

-produce_data: Is a function that is borne by a material entity by virtue of its structure. When realized the material entity produces (has an output of) data

• As a result of the data_functions, the definition of instrument could be changed to "is a device that is designed with the intention to provide the function to produce_data
• DS: I think produce_data is still too restrictive: An ultrasonic homogenizer is an instrument and does not produce data. Again, a more appropriate differentiae would be instrument has parameter (be it an on/off switch in the simplest case or software in a more complex case).

• Continuation of the has_model_number/identifies<->identified_by discussion here.

[Melanie Courtot]

Hi,

Possible additions to the agenda:

-  manufacturer use case (cf agenda 14 october)

- discuss difference between device and instrument and do we need to keep both. I am unclear about the distinction: for example Frank seems to say an ultrasonic homogenizer is a device whereas Daniel would say it's an instrument. Also, I'm unsure with that we gain something by saying for example an ultrasonic homogenizer is an instrument vs saying it is a device.  Why do we need the distinction?

(cf also email from Alan)

I did add those to the agenda on the wiki as well.

I hope you are fully recovered Daniel, talk to you tomorrow :)

Melanie

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