Conference calls instrument 2007-2008

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Summary of the Instrument Branch Conference Calls

This is the agenda of the conference calls for the branch Instrument. You can read through the notes of these calls on the notes page of 2007 and 2008.

Agenda for 2nd. December 2008

  • manufacturer use case (cf agenda 14 october)
  • discuss difference between device and instrument and do we need to keep both. I (MC) am unclear about the distinction: for example Frank seems to say an ultrasonic homogenizer is a device whereas you 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.
  • 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, an additional differentiae would be instrument has parameter (be it an on/off switch in the simplest case or software in a more complex case), range= IAO_0000140:setting datum. But this is still not enough, since there are devices where you can adjust e.g. a simple scale, and the majority might still consider these devices not instruments. I guess its just a matter of complexity or parts that need to work together to fulfil a function.
  • Continuation of the has_model_number/identifies<->identified_by discussion here.

Minutes


Agenda for 18. November 2008

  1. the name of the relation,
  2. the relation definition,
  3. the domain and range,
  4. example of use
  5. Then submit a tracker item for each one
  • List of Relations from MO that are relevant to the ObiBranch Instrument

Image:InstrumentRelationsFromMO.txt

runs OS/software

  • Domain: any sufficient automated and computerized subclass of OBI:instrument and OBI:platform
  • Range: a realizable_entity subclass (equivalent to the deleted OBI:software)

realizes process step

  • Domain: OBI:instrument
  • Range: some BFO:processual enity subclass, such as BFO:Process, BFO:fiat process part, OBI:protocol_application or OBI:assay ?

or alternatively (dept. on granularity) executes

  • Domain: OBI:instrument
  • Range: BFO:process, OBI:assay

has_function

  • Domain: OBI:instrument
  • Range: OBI:instrument_function

measures

  • Domain: OBI:instrument, OBI:partofinstrument OR we have a class OBI:instrument_application here...
  • Range: OBI:data_object

parameter_setting

  • Domain: OBI:instrument
  • Range: OBI:parameter_value_application

(or additionaly) default_setting

  • Domain: OBI:instrument
  • Range: OBI:parameter_value_application

data_input

  • Domain: OBI:instrument
  • Range: OBI:data_object, OBI:data_set

data_output

  • Domain: OBI:instrument
  • Range: OBI:data_object, OBI:data_set

has_vendor

  • Domain: OBI:instrument
  • Range: vendor (not yet present in OBI)

has_model

  • Domain: OBI:instrument
  • Range: model (not yet present in OBI)

throughput_style (highthroughput vs small scale)

  • Domain: OBI:instrument
  • Range: datathroughputscale (not yet present in OBI)

part_of_system/platform/pipeline

  • Domain: OBI:instrument
  • Range: OBI:platform

placement/environment (external influences)

  • Domain: OBI:instrument
  • Range: BFO:threedimensionalregion, BFO:site

user

  • Range: OBI:investigator or OBI:subject_role (are realizables/roles right now, so seem a bit strange), maybe better some Continuant 'person' class ?

(eventually) last_user

  • Domain: OBI:instrument
  • Range: OBI:investigator or OBI:subject_role (are realizables/roles right now, so seem a bit strange), maybe better some Continuant 'person' class ?

last-checked

  • Domain: OBI:instrument
  • Range: BFO:temporal instant

known_defects/problems/shortcomings

  • Domain: OBI:instrument
  • Range: (-), might be of datatype property (String)

processing_time/timescale

  • Domain: OBI:instrument
  • Range: BFO:temporal_interval

consumes

  • Domain: OBI:instrument
  • Range: OBI:labware/consumables


There could be more abstract relations, i.e. to an 'Instrumentation Effect' class (as in EXPO) that describes what implecations regarding the design princlipe lie in a decision to use a specific instrument type...


  • 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.


Minutes


Agenda for 14. October 2008

Minutes


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 ?

Minutes


Call of 22. July 2008 skipped due to ISMB


Agenda for 15. July 2008

Minutes


Agenda for 1. July 2008

Minutes


Agenda for 17. June 2008

Minutes


Agenda for 10. June 2008:

if time permits:

Minutes


03. June 2008

Minutes


20. and 27. May 2008 (skipped)


13. May 2008

Agenda:

  • Check new Branch Report items
  • Add and discuss new terms provided by Phillippe
  • 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
  • Minutes


6. May 2008

Agenda:

  • Review latest changes implemented by Frank and Melanie in owl file due to branch report.
  • Clean up remaining issues as found on http://sw.neurocommons.org/2008/obi/reports/InstrumentAndPart_report.html
  • Review status of Function/PA discussions: (Should we or the Function branch review? Frank could you summarize the outcome of your discussion with Bjoern?)
    • e.g. For each instrument I with function F there is a protocol PR each application P of which has_participant instrument I which realizes its function F as part of P.
    • instrument I 'has minimal functional realization' in protocol application PF. We can then later automatically translate PF --> F (e.g. heating --> 'heating_function') to create the instrument function hierarchy in parallel.
  • next steps would be to
    • a) convert the function terms from the instrument branch to PF terms, and submit them to the protocol application branch (if they don't exist there already).
    • b) create the relation 'minimal functional realization of' in the relation branch
    • c) connect instruments with their PF protocol applications using the relation b)
    • d) write a script that will auto-create the function terms based on a - c
    • Example of outcome:
      • Pipetting is a protocol_application (material separation) with the objective to obtain a defined volume of liquid material (output) from a larger volume of input liquid material utilizing a pipette device.
      • Pipetting_function is a function that is realized in a pipetting protocol_application
      • Pipette has function pipetting function
  • Add missing definitions for device functions on http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
  • Minutes


22. & 29. April 2008

skipped


15. April 2008

Agenda:

  • review what BFO has to say about Function definitions (bill? + email of 29/03/2008 06:23 to Barry))
    • e.g. we link to function via a "bearer_of" SOME bfo:function owl:Restriction
    • Protocol_application would do the same via "realizes" SOME bfo:function owl:Restriction
    • For each instrument I with function F there is a protocol_application P that has_participant instrument I which realizes function F as part of P.
    • Functions sould get all the OBI required metadata including definitions of the bfo:function
  • review new colums added to the left of the device fct spreadsheet at http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en
    • has_bearer range (as derived from def), to populate device top level
    • bearer-superclass (shall we start to add these in the owl file?)
  • add further BFO compliant definitions
  • Minutes


8. April 2008

  • skipped


1. April 2008

Agenda:

  • review what BFO has to say about Function definitions
  • review Bills email to Barry: "Since the branch imports BFO, they can certainly build off the bfo:function there. They would then link to that function via a "bearer_of" SOME bfo:function owl:Restriction"
  • review alternative function modelling strategies (borders to roles, protocol application (processes) and relations) as far as our needs and table is regarded.
  • review Functions definitions on

http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en


25. March 2008

Easter Break - No call -


18. March 2008

Agenda:

  • review last weeks action items:
    • Flow Cytometer definition based on its parts (Frank)
    • review Functions on

http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en (Bill?)

  • continue to extract important upper level instrument functions from device hierarchy for later crossproduct generation.
  • Minutes


11. March 2008

Agenda:

http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en


04.March 2008

  • Discussion about using defined classes for our instruments.
  • Discussion about functions

AI:
- Frank will define Flow Cytometer and Mass Spectrometer based on their parts
- Ryan will provide a definition of "sorter"
- Bill will review the google spreadsheet for functions http://spreadsheets.google.com/ccc?key=pT8ShyqlllIVSL43Cm6zRBQ&hl=en and comment during next call

26.February 2008


19.February 2008:

  • Agenda:
    • re-check rel list on http://spreadsheets.google.com/ccc?key=p4ViR8BgYUWaAG1b5IaxcJw&hl=en (complete? Defs good?)
    • play with device is_manufactured_by some (organization or person) crossproduct
    • ?interrogation_point (Ryan?)
    • ?jet_in_air_flow_chamber
    • identify basic instrument functions for needed crossproducts (compound instrument names) to sort out our 'upper level'
    • define next steps before release
  • Minutes


12.February 2008:


05. February 08:


22. January 08:

  • Agenda:
    • Add still missing definitions and examples to our list of relations in the google spreadsheet
    • Summarize instrument branch developments, open and upcoming issues for Ryan/Melanie to present at WS
  • Minutes


15. January 07:

  • Agenda:
    • Add definitions to our list of relations
    • Discuss metadata name issues on citation vs source and cardinality
    • Instrument use case discussion
    • Resolve problems with 'question-marked' classes.
    • Discuss policy to mark Meta-classes/helper classes via '_'-prefix.
  • Minutes


11. December 07:

  • Agenda:
    • Discuss metadata name issues on citation vs source
    • Discuss cardinality of above
    • Discuss term update results/issues, e.g.
      • "cardinal_part_of_instrument" class now seems out of place which is not even classified as a device.
    • Instrument use case discussion
    • Resolve problems with 'question-marked' classes.
    • Discuss policy to mark Meta-classes/helper classes via '_'-prefix.
    • ???

04. December 07:

  • Agenda:
    • Defined classes discussion
    • OBI software?
    • Milestones


27. November 07:

  • Agenda:
    • Instrument leaf node definition discussion
    • Instrument use case discussion
    • Resolve problems with 'question-marked' classes.
    • Discuss policy to mark Meta-classes/helper classes via '_'-prefix.
    • Discuss the 'new' relations for instruments and mappings
    • Minutes


  • 20. November 07:
  • Agenda:
    • Instrument leaf node definition discussion continued

No call today, discussion about the leaf nodes continues on obi-devel list.


  • 13. November 07:
  • Agenda:
    • Instrument leaf node definition discussion
    • Instrument use case discussion
    • Discuss exploitation of usable ISO standards, e.g.
      • ISO 15225:2000 Nomenclature -- Specification for a nomenclature system for medical devices for the purpose of regulatory data exchange
      • ISO/IEEE 11073-10101:2004 Health informatics -- Point-of-care medical device communication -- Part 10101: Nomenclature
      • ISO/TS 20225:2001 Global medical device nomenclature for the purpose of regulatory data exchange
    • Minutes


  • 6. November 07:
  • Agenda:
    • Resolve problems with questions marked classes.
    • Metadata discussion (What are the defaults)?
      • Discuss if we need arestotelian definitions for leaf node terms.


  • 30. October 07:
  • Agenda:
    • Discuss obi naming policy regarding homonyms and true name redundancy (see email correspondence)
    • Discuss automatic addition of metadata/other checks, e.g. do we need a policy how to capture Editors names (in initials vs. full names)
      • What else could be useful to check?


  • 23. October 07:
  • Agenda:
    • Discuss general development policies
    • Discuss obi metadata
    • Discuss automatic addition of metadata/other checks


  • 16. October 07:
  • Agenda:
    • Discuss general development policies
    • Enable Melanie to svn update and commit.
    • Discuss obi metadata


  • 9. October 07:
  • Agenda:
    • Enable Melanie to modify and save the changes in the svn Instruments branch.owl file.
    • Discuss the latest relations branch developments with respect to instrument relations, i.e. from last Fridays relations call notes: "We discussed the issue of how to relate the operator of an instrument to the instrument. We discussed the possibility that it would be something like a process in which the operator had an "operator role" and the instrument the "operated role". Still it seems this may not be enough."


  • 2. October 07:
  • Agenda:
    • Give an overwiew on our branch to our new participant Melanie.
    • Minutes


  • 25. September 07:
  • Agenda:
    • Discuss handling of our required relations in relations branch (we have to respond to the relations branch with our comments):
      • instrument "executes" process & assay: already there as "is_instrument_for"
      • has_manufacturer was changed to alternate term "is_manufactured_by", which is now in obi trunk
      • has_make is the same as is_manufactured_by organization or person
    • Add new terms (Array, Array Group, Hardware) that came from the Relations branch (as requested by MO)
    • Add new terms submitted from PA branch:
      • electrophoresis box:a specifically configured apparatus used in protocol applicatyions to seperate charged molecules in an electric field across a porous matrix or medium. Example:CHEF gel box, slab gel box, capillary electrophoresis
      • power pack: a specifically configured apparatus permitting the defined application of an electrical charge to an electrophoresis apparatus for a protocol application involving electrophoresis. The power pack may permit the defined application of a given amount of current for a defined length of time, Example: Power pack, CHEF gel box
      • fluorometer: an instrument for the detection and measurement of fluoresence, Example: laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
    • Discuss and refine cardinal part of instruments hierarchy
    • Discuss next steps and deadlines
    • Minutes


  • 4. September 07:
  • Agenda:
    • Add new terms submitted from PA branch and relations branch
    • Discuss object upper level
    • Go over the file and resolve problems with classes marked with "?"
    • Discuss next steps, e.g.
      • adding all metadata
      • how and where to get more terms


  • 21. August 07:
  • Agenda:
    • Implication of 'artifact' / 'biomaterial' work on our upper level
    • Resolve problems with last classes marked "?"
    • Check if all classes comply with naming conventions
    • Discuss next steps, e.g.
      • adding metadata
      • how and where to get more terms,
      • how to encourage people to participate
    • Minutes


  • 14. August 07:
  • Agenda:
    • Checkout latest OBI-svn with all the latest changes (BFO1.0 to 1.1 update)
    • Hear about outcome of 'artifact' / 'biomaterial' discussion on obi-dev list (Frank will present 'object' upper level)
    • Go over the file and resolve problems with classes marked with "?"
    • Check if all classes comply with naming conventions
    • Discuss next steps, e.g.
      • refining top level,
      • adding metadata,
      • how and where to get more terms,
      • how to encourage people to participate
    • Minutes


  • 17July2007
    • Agenda:
      • Checkout latest OBI-svn with all the latest changes
      • Review on issues that came up during WS and that affect our branch and look at action items from WS on https://wiki.cbil.upenn.edu/obiwiki/index.php/Bethesda_Meeting_Summary_and_Conclusions , e.g.:
      • 5. Instrument branch: improve the definition of the platform,
      • 6. Instrument branch: address reagent part to deal with computational platform where no typical reagents are used and to include being put together for a purpose. Should not include vendor. Will now be included in OWL file to aid editing - AR will do that.
      • 7. Instrument branch: ProtocolApplication what is the platform used for (Instrument/PA branches)
      • 8. Instrument branch: Resolve issues with artefact and biomaterial overlap in definitions (all)
      • 9. Instrument branch: Remove device and create as a synonym for instrument (Instrument)
      • 18. Artefact object discussion. Two different hierarchies were discussed. No resolution during meeting. These OWL files need to be posted and discussed during a dev call
      • 29. Helper classes for temporary terms. All branches will use branchname_temp (all)
    • Minutes
  • 3July2007
    • Agenda:
      • Everyone should svn checkout (and learn to work with) the updated branched OBI.owl (see https://svn.sourceforge.net/svnroot/obi/branchDevelopment/trunk/instructions-svn-local.txt ).
      • Discuss the questionable classes (marked wit a "?" prefix) and corresponding editor_notes.(including mass_spectrometry_instrument)
      • Identify instrument-branch presenter for OBI WS.
      • Discuss the term artefact, instrument and device definitions.
      • Discuss the flow_cytometer functions and possible ways to categorize flow_cytometers accordingly.
    • Minutes
  • 19June2007
    • Agenda:
      • Review latest OWL File for hierarchy
      • Discuss the term artefact
      • Add intermediate classes
    • Minutes
  • 12June2007
    • Agenda:
  • 5June2007
    • Agenda:
      • Update on Action Items from last call
      • Discuss changes needed in Instrument branch file
      • Who will be on the developers call tomorrow?
      • See [[ Conference_calls_instrument_2007_notes|Minutes]] for details.
  • 29May2007
    • Agenda:
      • Update on Action Items from last call
      • Discuss changes needed in Instrument branch file
      • See Minutes | for details.
  • 15May2007
      • No call
  • 8May2007
    • Agenda:
      • Discuss items needed before loading terms from the Master Excel file into the OBI Instrument branch OWL file
      • Update from PSI meeting re:terms from this community
      • See [[ Conference_calls_instrument_2007_notes|Minutes |]] for details.
  • 1May2007
    • Agenda:
      • Continue to review Instrument Master Term list file for terms relevant for this branch
      • Update from PSI meeting re:terms from this community - Tentative
  • 24Apr2007
    • Agenda:
      • Continue to review Instrument Master Term list file for terms relevant for this branch
      • Cancelled due to lack of attendance
  • 17Apr2007
    • Agenda:
      • Discuss Ryan's list of 300 terms, marking those that do not actually belong to the Instrument branch (and who we need to email about it
      • Next call is next week, Tuesday, same time. Marked on OBI Google Calendar.
      • See Minutes | for details.
  • 29Mar2007
    • Agenda:
      • Discuss 'labware'
      • Discuss a proposed 'labware' - 'container' synonymy according to list of labware that are not containers Daniel compiled.
      • Discuss added instrument terms on wiki
      • Plan next call.
      • See [[ Conference_calls_instrument_2007_notes|Minutes |]] for details.


  • 16Mar2007 
 * Agenda:
   * Review the scope of this section of OBI
   * Discuss definitions for the proposed terms, e.g. Device, Equipment etc.
   * Start to bin terms into categories if time permits
   * Plan next call
 * Action Items:
   * All - review existing posted Instrument terms to see if the proposed definitions are precise enough to bin the terms under a single parent.
 * See Minutes for details.
  • 12Mar2007 
 * Agenda: Review Items on InstrumentIssues wiki page
 * Action Items:
   * DS - post UMLS terms that may help to organize instrument terms
   * All - work on a more general definition for OBI.
 * See Minutes for details.
  • 09Mar2007 
 * Agenda:
   * Review current proposed terms
 * Action Items:
   * None
 * See [[ Conference_calls_instrument_2007_notes|Minutes |]] for details.
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