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obi-protocol-application-branch — Discussion of terms that are in the Protocol Application branch of OBI.
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-30 10:52:20
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Hi again,
Following Alan's note on obsolete relation, I am going over the protocol
application branch and checking restrictions:
I have so far spotted a few errors such as
DNA sequence feature detection:
has_specified_input some 'double-stranded DNA' or
DNA sequence variation detection:
has_specified_input some 'ribonucleic acids' **
but the more important is the following:
*animal feeding* has currently the following restriction: realizes some
'feed role' , which should probably be replaced by:
realizes some ('feed role' and (inheres_in some 'material_entity'))....
or should it be
has_specified_input some (material_entity and (realizes some 'feed role'))
Classifier likes either but I guess it is more than a simple question of style. Bjoern had pointed to frequent abuse of 'has_specified_input' relation.
I have found myself confronted with this issue with several classes already (e.g. elution...)
s already (e.g. elution with a restriction such as has_specified_input some ('{molecular entities, molecular entity}' and (has_role some 'solvent role')))
Cheers
--
Philippe Rocca-Serra, PhD
Technical Coordinator
www.ebi.ac.uk/net-project
The European Bioinformatics Institute email: ro...@eb...
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
--
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-30 10:30:46
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Hi James > The scope is derived from what we need for the GenePattern use case. > If you have some use case or examples of things you would want in I > think we should take a look at them. We don't require anything as > granular as you specify here so far, but this is not to say we > shouldn't have them in. For the example above I would probably like to > abstract out as much as possible so we don't get too caught up in the > specifics. For glucose concentration values, it would be good if we > could abstract this to a data item or set by the features that define > it and link that class of data item/set to an appropriate list of data > visualizations. I am with you here and have actually used measured data item for that matter. The modeling should deliver a generic solution . thx P |
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From: James M. <ma...@eb...> - 2009-07-30 10:18:12
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Hi Phil, Answers in line: Philippe Rocca-Serra wrote: > Hi James, > > I am looking at the link and have the following suggestion/request: > > i. gene list visualization: > > Can we think of a more generic term such as 'molecular entity list > visualization' so that protein lists, metabolite lists could be handled ? Definitely, we can add a parent class to this which is able to visualize various mol entities we desire. > > ii. then another question, related to the 'visualization', have you > discussed how to specify what is plotted against what or is it out of > scope for the moment? > > for example, I am currently modeling 'glucose tolerance test' and I > want to say that I 'visualizing/plotting' ]glucose concentration > values (realizing/concretizing 'dependent variable specification'] as > a function of [time values (realizing/concretizing 'dependent variable > specification' )]. > The scope is derived from what we need for the GenePattern use case. If you have some use case or examples of things you would want in I think we should take a look at them. We don't require anything as granular as you specify here so far, but this is not to say we shouldn't have them in. For the example above I would probably like to abstract out as much as possible so we don't get too caught up in the specifics. For glucose concentration values, it would be good if we could abstract this to a data item or set by the features that define it and link that class of data item/set to an appropriate list of data visualizations. > > iii. This is more a term request related question: > > Should DT include terms such as 'area calculation' (and corresponding > 'area calculation objective') since we have (mean calculation) and > then possibly add 'integration data transformation' Sure let's get these in, I think it would be useful. Cheers, James > > (if this is valid and not causing too much of a scope creep, I would > need terms to cover derivation/differentiation) > > Let me know and i'll provide all metadata > > cheers > > P > > > James Malone wrote: >> Hi All, >> >> Just a reminder, I'm adding in some of the visualization terms into >> OBI this week as these are urgent for the OBI manuscript. If anyone >> has anything they'd like to contribute please add to the spreadsheet >> here >> http://spreadsheets.google.com/ccc?key=0Ak22gS-WQteedGdvQUtqOWM5dVBjc3p4TjcyaWNPYkE&hl=en >> >> >> Cheers, >> >> James >> >> >> > > -- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom Tel: + 44 (0) 1223 494 676 Fax: + 44 (0) 1223 492 468 |
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-30 10:10:33
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Hi James, I am looking at the link and have the following suggestion/request: i. gene list visualization: Can we think of a more generic term such as 'molecular entity list visualization' so that protein lists, metabolite lists could be handled ? ii. then another question, related to the 'visualization', have you discussed how to specify what is plotted against what or is it out of scope for the moment? for example, I am currently modeling 'glucose tolerance test' and I want to say that I 'visualizing/plotting' ]glucose concentration values (realizing/concretizing 'dependent variable specification'] as a function of [time values (realizing/concretizing 'dependent variable specification' )]. iii. This is more a term request related question: Should DT include terms such as 'area calculation' (and corresponding 'area calculation objective') since we have (mean calculation) and then possibly add 'integration data transformation' (if this is valid and not causing too much of a scope creep, I would need terms to cover derivation/differentiation) Let me know and i'll provide all metadata cheers P James Malone wrote: > Hi All, > > Just a reminder, I'm adding in some of the visualization terms into OBI > this week as these are urgent for the OBI manuscript. If anyone has > anything they'd like to contribute please add to the spreadsheet here > http://spreadsheets.google.com/ccc?key=0Ak22gS-WQteedGdvQUtqOWM5dVBjc3p4TjcyaWNPYkE&hl=en > > Cheers, > > James > > > -- Philippe Rocca-Serra, PhD Technical Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: ro...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 Cambridge CB10 1SD, UK room: A3-141 -- |
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From: Bjoern P. <bp...@li...> - 2009-07-28 19:40:32
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Ah, I misunderstood your point about complex. I think that means we should request the term DNA polymerase from PRO + all the subclasses you need. ----- Original Message ----- From: "Philippe Rocca-Serra" <ro...@eb...> Cc: "OBI Developers" <obi...@li...>, "Protocol App Branch" <obi...@li...> Sent: Tuesday, July 28, 2009 9:31:45 AM GMT -08:00 US/Canada Pacific Subject: Re: [Obi-devel] DNA sequencing Bjoern Peters wrote: > - DNA polymerase is already imported under protein complex. From GO as suggested > What is imported in 'DNA polymerase complex', which would mean that there are part which may be specified. Taq polymerase is a DNA polymerase with DNA polymerase activity but I don't think it is a DNA polymerase complex (as currently defined by OBI definition of a complex). We could potentially refer to the Klenow Fragment of DNA polymerase I, which again is not a complex. This is what I was trying to point at. I guess using 'DNA polymerase or DNA polymerase complex' on the restriction would solve the problem. > - Agree with Frank that the 'has specified ... ' relations should have been cleaned up and not refer to roles any more. I created a ticket for Larissa. > - I thought at the workshop we wanted to create the 'has specified participant' relation, which was to be used for reagents / instruments etc. which are not necessarily present at the start of the process, and more importantly aren't the things transformed into outputs. > This is still fine for the time being. I will used those relations as place holders and carry out the fixes as soon as those more refined relations are phased in. cheers Philippe > > > > ----- Original Message ----- > From: "Frank Gibson" <fg...@gm...> > To: "Philippe Rocca-Serra" <ro...@eb...> > Cc: "OBI Developers" <obi...@li...>, "Protocol App Branch" <obi...@li...> > Sent: Tuesday, July 28, 2009 4:42:49 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Obi-devel] DNA sequencing > > > > > > On Tue, Jul 28, 2009 at 12:14 PM, Philippe Rocca-Serra < ro...@eb... > wrote: > > > Hi Frank > > > > > > yes, what is the issue here? We have the function catalytic_activity > > The thing is that, based on the information I have collected from manufacturers, I am pretty sure that DNA ligase (protein) is added (more precisely it should be T4 phage DNA ligase)) > and the DNA polymerase is added. A Complex as indicated by the definition is comprised of 2 or more subunits. We may want to set restrictions on those classes to formally distinguish > protein complex from the rest. > I think I am simply missing DNA polymerase in OBI at the moment,: it may be imported from...well this is where it can be difficult to decide. or just as for current DNA ligase, we create a class in OBI but I 'd rather not assert this in OBI since I feel it could live happily in another resource and we should mireot it. > > DNA polymerase exists in GO, so we should MIREOT it > > > > > > > > > > > I am not sure I follow. If you say immobilization is preceeded_by amplification then you have said that immobilization is 1 and amplification is 2. > I am only saying that Sequencing is 'preceded_by immobilization' and is_preceded_by 'amplification'. I guess I need to change to restriction to > preceded_by some ( 'immobilization' preceded_by some 'amplification') > > I think you need to include the part_of relation here, (has_part and preceded_by) > > Frank > > > > > > > > > > Those steps allow to distinguish Helicos sequencing (single > molecule sequencing no amplification needed) from Solexa or Solid > methods where an emulsion PCR is used for amplification > > > They are two distinct process which could be represented by the following > > Helicos sequencing has_part single_molecule_sequencing > > Solexa has_part single_molecule_sequencing preceeded_by (has_part amplification) > > > (no guarantee that actually reasons though :) > > I am currently adding the different libraries (paired end ditag library or single fragment library) to the biomaterial branch and I will need to add 'library construction' as a planned process. > > > > > > > >> I believe that it should be added that these processes achieve >> > planned > >> objective: sequence feature identification objective. >> >> > +1. I overlooked this. will add. > > Bjoern pointed out that a range of information might also require > attention in the realm of genome assembly in order to have the > capability to indicate 'redundancy and fold coverage or number of > contigs and so forth. > These are information that matters to Dawn Field and the people behind > the Genome Standard Consortium. > > > Can you present this information in the form of concrete case-studies and use-case please. > > thanks for the input > > P > > > > -- Philippe Rocca-Serra, PhD Technical Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: ro...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 Cambridge CB10 1SD, UK room: A3-141 -- ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Obi-devel mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-devel |
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-28 16:32:02
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Bjoern Peters wrote: > - DNA polymerase is already imported under protein complex. From GO as suggested > What is imported in 'DNA polymerase complex', which would mean that there are part which may be specified. Taq polymerase is a DNA polymerase with DNA polymerase activity but I don't think it is a DNA polymerase complex (as currently defined by OBI definition of a complex). We could potentially refer to the Klenow Fragment of DNA polymerase I, which again is not a complex. This is what I was trying to point at. I guess using 'DNA polymerase or DNA polymerase complex' on the restriction would solve the problem. > - Agree with Frank that the 'has specified ... ' relations should have been cleaned up and not refer to roles any more. I created a ticket for Larissa. > - I thought at the workshop we wanted to create the 'has specified participant' relation, which was to be used for reagents / instruments etc. which are not necessarily present at the start of the process, and more importantly aren't the things transformed into outputs. > This is still fine for the time being. I will used those relations as place holders and carry out the fixes as soon as those more refined relations are phased in. cheers Philippe > > > > ----- Original Message ----- > From: "Frank Gibson" <fg...@gm...> > To: "Philippe Rocca-Serra" <ro...@eb...> > Cc: "OBI Developers" <obi...@li...>, "Protocol App Branch" <obi...@li...> > Sent: Tuesday, July 28, 2009 4:42:49 AM GMT -08:00 US/Canada Pacific > Subject: Re: [Obi-devel] DNA sequencing > > > > > > On Tue, Jul 28, 2009 at 12:14 PM, Philippe Rocca-Serra < ro...@eb... > wrote: > > > Hi Frank > > > > > > yes, what is the issue here? We have the function catalytic_activity > > The thing is that, based on the information I have collected from manufacturers, I am pretty sure that DNA ligase (protein) is added (more precisely it should be T4 phage DNA ligase)) > and the DNA polymerase is added. A Complex as indicated by the definition is comprised of 2 or more subunits. We may want to set restrictions on those classes to formally distinguish > protein complex from the rest. > I think I am simply missing DNA polymerase in OBI at the moment,: it may be imported from...well this is where it can be difficult to decide. or just as for current DNA ligase, we create a class in OBI but I 'd rather not assert this in OBI since I feel it could live happily in another resource and we should mireot it. > > DNA polymerase exists in GO, so we should MIREOT it > > > > > > > > > > > I am not sure I follow. If you say immobilization is preceeded_by amplification then you have said that immobilization is 1 and amplification is 2. > I am only saying that Sequencing is 'preceded_by immobilization' and is_preceded_by 'amplification'. I guess I need to change to restriction to > preceded_by some ( 'immobilization' preceded_by some 'amplification') > > I think you need to include the part_of relation here, (has_part and preceded_by) > > Frank > > > > > > > > > > Those steps allow to distinguish Helicos sequencing (single > molecule sequencing no amplification needed) from Solexa or Solid > methods where an emulsion PCR is used for amplification > > > They are two distinct process which could be represented by the following > > Helicos sequencing has_part single_molecule_sequencing > > Solexa has_part single_molecule_sequencing preceeded_by (has_part amplification) > > > (no guarantee that actually reasons though :) > > I am currently adding the different libraries (paired end ditag library or single fragment library) to the biomaterial branch and I will need to add 'library construction' as a planned process. > > > > > > > >> I believe that it should be added that these processes achieve >> > planned > >> objective: sequence feature identification objective. >> >> > +1. I overlooked this. will add. > > Bjoern pointed out that a range of information might also require > attention in the realm of genome assembly in order to have the > capability to indicate 'redundancy and fold coverage or number of > contigs and so forth. > These are information that matters to Dawn Field and the people behind > the Genome Standard Consortium. > > > Can you present this information in the form of concrete case-studies and use-case please. > > thanks for the input > > P > > > > -- Philippe Rocca-Serra, PhD Technical Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: ro...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 Cambridge CB10 1SD, UK room: A3-141 -- |
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From: Bjoern P. <bp...@li...> - 2009-07-28 16:02:54
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- DNA polymerase is already imported under protein complex. From GO as suggested - Agree with Frank that the 'has specified ... ' relations should have been cleaned up and not refer to roles any more. I created a ticket for Larissa. - I thought at the workshop we wanted to create the 'has specified participant' relation, which was to be used for reagents / instruments etc. which are not necessarily present at the start of the process, and more importantly aren't the things transformed into outputs. ----- Original Message ----- From: "Frank Gibson" <fg...@gm...> To: "Philippe Rocca-Serra" <ro...@eb...> Cc: "OBI Developers" <obi...@li...>, "Protocol App Branch" <obi...@li...> Sent: Tuesday, July 28, 2009 4:42:49 AM GMT -08:00 US/Canada Pacific Subject: Re: [Obi-devel] DNA sequencing On Tue, Jul 28, 2009 at 12:14 PM, Philippe Rocca-Serra < ro...@eb... > wrote: Hi Frank yes, what is the issue here? We have the function catalytic_activity The thing is that, based on the information I have collected from manufacturers, I am pretty sure that DNA ligase (protein) is added (more precisely it should be T4 phage DNA ligase)) and the DNA polymerase is added. A Complex as indicated by the definition is comprised of 2 or more subunits. We may want to set restrictions on those classes to formally distinguish protein complex from the rest. I think I am simply missing DNA polymerase in OBI at the moment,: it may be imported from...well this is where it can be difficult to decide. or just as for current DNA ligase, we create a class in OBI but I 'd rather not assert this in OBI since I feel it could live happily in another resource and we should mireot it. DNA polymerase exists in GO, so we should MIREOT it I am not sure I follow. If you say immobilization is preceeded_by amplification then you have said that immobilization is 1 and amplification is 2. I am only saying that Sequencing is 'preceded_by immobilization' and is_preceded_by 'amplification'. I guess I need to change to restriction to preceded_by some ( 'immobilization' preceded_by some 'amplification') I think you need to include the part_of relation here, (has_part and preceded_by) Frank Those steps allow to distinguish Helicos sequencing (single molecule sequencing no amplification needed) from Solexa or Solid methods where an emulsion PCR is used for amplification They are two distinct process which could be represented by the following Helicos sequencing has_part single_molecule_sequencing Solexa has_part single_molecule_sequencing preceeded_by (has_part amplification) (no guarantee that actually reasons though :) I am currently adding the different libraries (paired end ditag library or single fragment library) to the biomaterial branch and I will need to add 'library construction' as a planned process. > I believe that it should be added that these processes achieve planned > objective: sequence feature identification objective. > +1. I overlooked this. will add. Bjoern pointed out that a range of information might also require attention in the realm of genome assembly in order to have the capability to indicate 'redundancy and fold coverage or number of contigs and so forth. These are information that matters to Dawn Field and the people behind the Genome Standard Consortium. Can you present this information in the form of concrete case-studies and use-case please. thanks for the input P -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Obi-devel mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-devel |
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From: Frank G. <fg...@gm...> - 2009-07-28 11:43:02
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On Tue, Jul 28, 2009 at 12:14 PM, Philippe Rocca-Serra <ro...@eb...>wrote: > Hi Frank > > >> yes, what is the issue here? We have the function catalytic_activity >> >> The thing is that, based on the information I have collected from > manufacturers, I am pretty sure that DNA ligase (protein) is added (more > precisely it should be T4 phage DNA ligase)) > and the DNA polymerase is added. A Complex as indicated by the definition > is comprised of 2 or more subunits. We may want to set restrictions on those > classes to formally distinguish > protein complex from the rest. > I think I am simply missing DNA polymerase in OBI at the moment,: it may be > imported from...well this is where it can be difficult to decide. or just as > for current DNA ligase, we create a class in OBI but I 'd rather not assert > this in OBI since I feel it could live happily in another resource and we > should mireot it. DNA polymerase exists in GO, so we should MIREOT it > > > > >> I am not sure I follow. If you say immobilization is preceeded_by >> amplification then you have said that immobilization is 1 and amplification >> is 2. >> > I am only saying that Sequencing is 'preceded_by immobilization' and > is_preceded_by 'amplification'. I guess I need to change to restriction to > preceded_by some ( 'immobilization' preceded_by some 'amplification') I think you need to include the part_of relation here, (has_part and preceded_by) Frank > > > > >> Those steps allow to distinguish Helicos sequencing (single >> molecule sequencing no amplification needed) from Solexa or Solid >> methods where an emulsion PCR is used for amplification >> >> >> They are two distinct process which could be represented by the following >> >> Helicos sequencing has_part single_molecule_sequencing >> >> Solexa has_part single_molecule_sequencing preceeded_by (has_part >> amplification) >> >> >> (no guarantee that actually reasons though :) >> > > I am currently adding the different libraries (paired end ditag library or > single fragment library) to the biomaterial branch and I will need to add > 'library construction' as a planned process. > > > >> > I believe that it should be added that these processes achieve >> planned >> > objective: sequence feature identification objective. >> > >> +1. I overlooked this. will add. >> >> Bjoern pointed out that a range of information might also require >> attention in the realm of genome assembly in order to have the >> capability to indicate 'redundancy and fold coverage or number of >> contigs and so forth. >> These are information that matters to Dawn Field and the people behind >> the Genome Standard Consortium. >> >> >> Can you present this information in the form of concrete case-studies and >> use-case please. >> > > thanks for the input > > P > -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ |
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-28 11:14:32
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Hi Frank > > yes, what is the issue here? We have the function catalytic_activity > The thing is that, based on the information I have collected from manufacturers, I am pretty sure that DNA ligase (protein) is added (more precisely it should be T4 phage DNA ligase)) and the DNA polymerase is added. A Complex as indicated by the definition is comprised of 2 or more subunits. We may want to set restrictions on those classes to formally distinguish protein complex from the rest. I think I am simply missing DNA polymerase in OBI at the moment,: it may be imported from...well this is where it can be difficult to decide. or just as for current DNA ligase, we create a class in OBI but I 'd rather not assert this in OBI since I feel it could live happily in another resource and we should mireot it. > > I am not sure I follow. If you say immobilization is preceeded_by > amplification then you have said that immobilization is 1 and > amplification is 2. I am only saying that Sequencing is 'preceded_by immobilization' and is_preceded_by 'amplification'. I guess I need to change to restriction to preceded_by some ( 'immobilization' preceded_by some 'amplification') > > Those steps allow to distinguish Helicos sequencing (single > molecule sequencing no amplification needed) from Solexa or Solid > methods where an emulsion PCR is used for amplification > > > They are two distinct process which could be represented by the following > > Helicos sequencing has_part single_molecule_sequencing > > Solexa has_part single_molecule_sequencing preceeded_by (has_part > amplification) > > > (no guarantee that actually reasons though :) I am currently adding the different libraries (paired end ditag library or single fragment library) to the biomaterial branch and I will need to add 'library construction' as a planned process. > > > I believe that it should be added that these processes achieve > planned > > objective: sequence feature identification objective. > > > +1. I overlooked this. will add. > > Bjoern pointed out that a range of information might also require > attention in the realm of genome assembly in order to have the > capability to indicate 'redundancy and fold coverage or number of > contigs and so forth. > These are information that matters to Dawn Field and the people behind > the Genome Standard Consortium. > > > Can you present this information in the form of concrete case-studies > and use-case please. thanks for the input P |
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From: Frank G. <fg...@gm...> - 2009-07-28 10:20:45
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On Tue, Jul 28, 2009 at 5:30 AM, Philippe Rocca-Serra <ro...@eb...>wrote: > Hi Alan, > > Thanks for the feedback. really helpful. > > > I don't like the has_agent relation. It is very ambiguous and I've > > been trying to get it removed from RO. I see that you want to use it > > to make the difference between sequencing by ligation and sequencing > > by synthesis, but I think we need to find a different way. I will > > think some about how. > > > > I've used it on purpose to prompt a reaction: Essentially what I wanted > to get at it the following: > Should the enzyme used in the sequencing reaction be described in the > same terms as the input DNA material? Yes, it is a specified_input > > I was looking at the definition of has_specific_input and it said the > following: > "The continuant realizes specified_Input_Role for that process. In > general, not all participants present at the beginning of the process > are specified_inputs." The text actuallly needs changing - we decided to exclude the notion of roles. This was the reason we dropped the has_specified_data_input relation. We must have overlooked updating the text, to something like "those entities specified as inputs in the plan/specicification > > Initially I used has_specific_input relation instead of has_agent, then > had second thoughts. > The DNA polymerase or DNA ligase does realize their role / function in a > sequencing process. yes, what is the issue here? We have the function catalytic_activity > > Side note: > I have used continuant 'DNA ligase' and continuant 'DNA polymerase > complex'. I am not too happy about the 'complex' thing so was thinking > of miroeting a 'DNA polymerase' > > > The specified output: information content entity, is way too general. > > As it is it could refer to getting a measurement of the mass of the > > supplied dna, for example, or a count of cpg islands, or behavioral > > assessments of the technicians who do the work. > > > Like I said, I was aware of this (and pointed to the classification of > PCR-SSCP assay as a consequence of 'information content entity' as too > general) > View this as placeholders that will be refined as more additions are > made to Information Content entities. > There was also a technical reason, I wanted to confine all my additions > to the PlanandPlannedProcesses.owl at the time of the editing. > > Definitions are missing. I know you say that metadata is not complete, > > but not having some indication of the scope of what you mean by the > > terms makes it hard to offer precise suggestions for improving the > > logical definitions. > You are right, I will work on those today. > > In particular, what are the boundaries of the > > process - are you thinking about one in which a vial of dna is input > > and a genome is output, or something at the chemical reaction level. > > Is any kind of preparation included in these processes or not? Do > > these processes included data transformations? > > > I am with you here. I have very fine grained representations for some of > the techniques, really drilling down. The work actually pointed to > interesting issues you picked upon. > When describing new sequencing techniques, I have included references to > key steps. For instance using preceded_by 'immobilization' and > preceded_by 'amplification of a clone' > but i could not find a way specify the order in which those steps would > occur. I am not sure I follow. If you say immobilization is preceeded_by amplification then you have said that immobilization is 1 and amplification is 2. > Those steps allow to distinguish Helicos sequencing (single > molecule sequencing no amplification needed) from Solexa or Solid > methods where an emulsion PCR is used for amplification They are two distinct process which could be represented by the following Helicos sequencing has_part single_molecule_sequencing Solexa has_part single_molecule_sequencing preceeded_by (has_part amplification) (no guarantee that actually reasons though :) > > Also, for a number of techniques, a sequence of subprocesses are > repeated (introduction of reagent mix, enzymatic reaction, washing, > imaging, clivage in a cycle which a run over and over) > How can we describe this 'motif' and these cycles ? create a defined class for this "motif" using has_part and preceeded_by. Then refer to it. Although each time you repeat the "motif in another process. I am assuming you are using the specified_output of the last time it was run, so you shoudl be able to link the different motifs in sequence based on the "named" specfied_output of the last run > > But more importantly, do we really need this level of detail ? hence the > scope issue. I've been conservative choosing to insist on the input (a > library of genomic DNA fragments, which needs to be added) and the > output (possibly images, then sequence reads). on this side, I am > confident that the discussion in IAO and SO will give us what we need > with a very good consistency. Just look at your use-case. Your use-case, and how it is used determines your scope, > > > I believe that it should be added that these processes achieve planned > > objective: sequence feature identification objective. > > > +1. I overlooked this. will add. > > Bjoern pointed out that a range of information might also require > attention in the realm of genome assembly in order to have the > capability to indicate 'redundancy and fold coverage or number of > contigs and so forth. > These are information that matters to Dawn Field and the people behind > the Genome Standard Consortium. > Can you present this information in the form of concrete case-studies and use-case please. Frank > > > That's it for now. > > > > Best, > > Alan > > > > > > > > > > > >> I'd like now to add various instruments and their suppliers (hence the > >> work on organization). > >> I will also need a number of materials (luciferase, various enzymes and > >> chemical with role of reagent) + I will aslo need role/function for > >> primer, adaptors and add processes related to clonal amplification and > >> library construction. > >> > >> And finally add metadata to those classes recently added. > >> > >> All comment welcome > >> > >> > >> Great to see some of you during ICBO meeting, I think it is been a good > >> meeting for OBI. > >> > >> -- > >> Philippe Rocca-Serra, PhD > >> > >> Technical Coordinator > >> www.ebi.ac.uk/net-project > >> > >> The European Bioinformatics Institute email: ro...@eb... > >> EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 > >> Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 > >> Cambridge CB10 1SD, UK room: A3-141 > >> -- > >> > >> > >> > ------------------------------------------------------------------------------ > >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > >> trial. Simplify your report design, integration and deployment - and > focus on > >> what you do best, core application coding. Discover what's new with > >> Crystal Reports now. http://p.sf.net/sfu/bobj-july > >> _______________________________________________ > >> Obi-devel mailing list > >> Obi...@li... > >> https://lists.sourceforge.net/lists/listinfo/obi-devel > >> > >> > > > -- > Philippe Rocca-Serra, PhD > > Technical Coordinator > www.ebi.ac.uk/net-project > > The European Bioinformatics Institute email: ro...@eb... > EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 > Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 > Cambridge CB10 1SD, UK room: A3-141 > -- > > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel > -- Frank Gibson, PhD http://peanutbutter.wordpress.com/ |
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-28 04:30:56
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Hi Alan, Thanks for the feedback. really helpful. > I don't like the has_agent relation. It is very ambiguous and I've > been trying to get it removed from RO. I see that you want to use it > to make the difference between sequencing by ligation and sequencing > by synthesis, but I think we need to find a different way. I will > think some about how. > I've used it on purpose to prompt a reaction: Essentially what I wanted to get at it the following: Should the enzyme used in the sequencing reaction be described in the same terms as the input DNA material? I was looking at the definition of has_specific_input and it said the following: "The continuant realizes specified_Input_Role for that process. In general, not all participants present at the beginning of the process are specified_inputs." Initially I used has_specific_input relation instead of has_agent, then had second thoughts. The DNA polymerase or DNA ligase does realize their role / function in a sequencing process. Side note: I have used continuant 'DNA ligase' and continuant 'DNA polymerase complex'. I am not too happy about the 'complex' thing so was thinking of miroeting a 'DNA polymerase' > The specified output: information content entity, is way too general. > As it is it could refer to getting a measurement of the mass of the > supplied dna, for example, or a count of cpg islands, or behavioral > assessments of the technicians who do the work. > Like I said, I was aware of this (and pointed to the classification of PCR-SSCP assay as a consequence of 'information content entity' as too general) View this as placeholders that will be refined as more additions are made to Information Content entities. There was also a technical reason, I wanted to confine all my additions to the PlanandPlannedProcesses.owl at the time of the editing. > Definitions are missing. I know you say that metadata is not complete, > but not having some indication of the scope of what you mean by the > terms makes it hard to offer precise suggestions for improving the > logical definitions. You are right, I will work on those today. > In particular, what are the boundaries of the > process - are you thinking about one in which a vial of dna is input > and a genome is output, or something at the chemical reaction level. > Is any kind of preparation included in these processes or not? Do > these processes included data transformations? > I am with you here. I have very fine grained representations for some of the techniques, really drilling down. The work actually pointed to interesting issues you picked upon. When describing new sequencing techniques, I have included references to key steps. For instance using preceded_by 'immobilization' and preceded_by 'amplification of a clone' but i could not find a way specify the order in which those steps would occur. Those steps allow to distinguish Helicos sequencing (single molecule sequencing no amplification needed) from Solexa or Solid methods where an emulsion PCR is used for amplification Also, for a number of techniques, a sequence of subprocesses are repeated (introduction of reagent mix, enzymatic reaction, washing, imaging, clivage in a cycle which a run over and over) How can we describe this 'motif' and these cycles ? But more importantly, do we really need this level of detail ? hence the scope issue. I've been conservative choosing to insist on the input (a library of genomic DNA fragments, which needs to be added) and the output (possibly images, then sequence reads). on this side, I am confident that the discussion in IAO and SO will give us what we need with a very good consistency. > I believe that it should be added that these processes achieve planned > objective: sequence feature identification objective. > +1. I overlooked this. will add. Bjoern pointed out that a range of information might also require attention in the realm of genome assembly in order to have the capability to indicate 'redundancy and fold coverage or number of contigs and so forth. These are information that matters to Dawn Field and the people behind the Genome Standard Consortium. > That's it for now. > > Best, > Alan > > > > > >> I'd like now to add various instruments and their suppliers (hence the >> work on organization). >> I will also need a number of materials (luciferase, various enzymes and >> chemical with role of reagent) + I will aslo need role/function for >> primer, adaptors and add processes related to clonal amplification and >> library construction. >> >> And finally add metadata to those classes recently added. >> >> All comment welcome >> >> >> Great to see some of you during ICBO meeting, I think it is been a good >> meeting for OBI. >> >> -- >> Philippe Rocca-Serra, PhD >> >> Technical Coordinator >> www.ebi.ac.uk/net-project >> >> The European Bioinformatics Institute email: ro...@eb... >> EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 >> Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 >> Cambridge CB10 1SD, UK room: A3-141 >> -- >> >> >> ------------------------------------------------------------------------------ >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> _______________________________________________ >> Obi-devel mailing list >> Obi...@li... >> https://lists.sourceforge.net/lists/listinfo/obi-devel >> >> -- Philippe Rocca-Serra, PhD Technical Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: ro...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 Cambridge CB10 1SD, UK room: A3-141 -- |
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From: Alan R. <ala...@gm...> - 2009-07-28 03:43:56
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On Mon, Jul 27, 2009 at 6:07 PM, Philippe Rocca-Serra<ro...@eb...> wrote: > Hi Everyone, > > as discussed with some of you during the ICBO conference, I did some > review and work towards sequencing. > It turns out that the restrictions were a bit off. More details can be > found in the log. > > I have added DNA sequencing as a defined class. I had currently to rely > on 'information content entity' as a specified output in the absence of > sequence (or read for that matter) but they will soon be available. I > have also distinguished DNA sequencing by use of DNA ligase from DNA > sequencing by use of DNA polymerase. > Created classes were pyrosequencing, chain termination sequence, SOLiD > sequencing. > > The classifier runs smoothly and interestingly places 'genotyping' as > currently defined as a kind of DNA sequencing which is correct. > It places PCR-SSCP assay as a kind of DNA sequencing but this is down to > the fact we don't yet enough shades under information entity (but these > are in the pipelines). > > There is still a lot of work to carry out. But before going further, I > wanted to give a heads up. It would be nice if OBI could cover > sequencing technology better since it is such a hot topic Indeed. And thanks for getting this started. Not surprisingly, I have some comments on the restrictions, with a mind to giving an idea where I think some of the work is. I don't like the has_agent relation. It is very ambiguous and I've been trying to get it removed from RO. I see that you want to use it to make the difference between sequencing by ligation and sequencing by synthesis, but I think we need to find a different way. I will think some about how. The specified output: information content entity, is way too general. As it is it could refer to getting a measurement of the mass of the supplied dna, for example, or a count of cpg islands, or behavioral assessments of the technicians who do the work. Definitions are missing. I know you say that metadata is not complete, but not having some indication of the scope of what you mean by the terms makes it hard to offer precise suggestions for improving the logical definitions. In particular, what are the boundaries of the process - are you thinking about one in which a vial of dna is input and a genome is output, or something at the chemical reaction level. Is any kind of preparation included in these processes or not? Do these processes included data transformations? I believe that it should be added that these processes achieve planned objective: sequence feature identification objective. That's it for now. Best, Alan > > I'd like now to add various instruments and their suppliers (hence the > work on organization). > I will also need a number of materials (luciferase, various enzymes and > chemical with role of reagent) + I will aslo need role/function for > primer, adaptors and add processes related to clonal amplification and > library construction. > > And finally add metadata to those classes recently added. > > All comment welcome > > > Great to see some of you during ICBO meeting, I think it is been a good > meeting for OBI. > > -- > Philippe Rocca-Serra, PhD > > Technical Coordinator > www.ebi.ac.uk/net-project > > The European Bioinformatics Institute email: ro...@eb... > EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 > Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 > Cambridge CB10 1SD, UK room: A3-141 > -- > > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Obi-devel mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-devel > |
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From: Philippe Rocca-S. <ro...@eb...> - 2009-07-27 22:08:00
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Hi Everyone, as discussed with some of you during the ICBO conference, I did some review and work towards sequencing. It turns out that the restrictions were a bit off. More details can be found in the log. I have added DNA sequencing as a defined class. I had currently to rely on 'information content entity' as a specified output in the absence of sequence (or read for that matter) but they will soon be available. I have also distinguished DNA sequencing by use of DNA ligase from DNA sequencing by use of DNA polymerase. Created classes were pyrosequencing, chain termination sequence, SOLiD sequencing. The classifier runs smoothly and interestingly places 'genotyping' as currently defined as a kind of DNA sequencing which is correct. It places PCR-SSCP assay as a kind of DNA sequencing but this is down to the fact we don't yet enough shades under information entity (but these are in the pipelines). There is still a lot of work to carry out. But before going further, I wanted to give a heads up. It would be nice if OBI could cover sequencing technology better since it is such a hot topic I'd like now to add various instruments and their suppliers (hence the work on organization). I will also need a number of materials (luciferase, various enzymes and chemical with role of reagent) + I will aslo need role/function for primer, adaptors and add processes related to clonal amplification and library construction. And finally add metadata to those classes recently added. All comment welcome Great to see some of you during ICBO meeting, I think it is been a good meeting for OBI. -- Philippe Rocca-Serra, PhD Technical Coordinator www.ebi.ac.uk/net-project The European Bioinformatics Institute email: ro...@eb... EMBL Outstation - Hinxton direct: +44 (0)1223 492 553 Wellcome Trust Genome Campus fax: +44 (0)1223 492 620 Cambridge CB10 1SD, UK room: A3-141 -- |
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From: Bjoern P. <bp...@li...> - 2009-07-09 14:29:07
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.. and future calls will be consolidated with other branches as discussed on the main mailing list. |
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From: Bjoern P. <bp...@li...> - 2009-07-02 15:36:32
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I will be on Centra + skype to see who can join (skype preferred). Agenda is (whatever needs to be done for the release, including): - follow up on workshop action items - integration of ONTIE terms ? - bjoern ----- Original Message ----- From: "Bjoern Peters" <bp...@li...> To: "Protocol App Branch" <obi...@li...> Sent: Wednesday, May 27, 2009 7:47:05 PM GMT -08:00 US/Canada Pacific Subject: [Obi-protocol-application-branch] call is ON To surprise everyone, I thought I should announce the call in advance again! Agenda is briefly - upcoming workshop - cloning terms worked on by Kevin and Bjoern - animal husbandry terms from Jennifer - vaccine terms from Oliver - Bjoern ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Obi-protocol-application-branch mailing list Obi...@li... https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch |
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From: Bjoern P. <bp...@li...> - 2009-05-28 02:47:35
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To surprise everyone, I thought I should announce the call in advance again! Agenda is briefly - upcoming workshop - cloning terms worked on by Kevin and Bjoern - animal husbandry terms from Jennifer - vaccine terms from Oliver - Bjoern |
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From: Bjoern P. <bp...@li...> - 2009-05-21 04:35:37
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I have a doctor appointment that I could not reschedule. |
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From: Bjoern P. <bp...@li...> - 2009-04-30 00:25:19
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Sorry for the late notice; I have a conflict I overlooked earlier. |
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From: Bjoern P. <bp...@li...> - 2009-04-23 14:34:08
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Sorry for the late notice. |
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From: Fostel, J. (NIH/N. [C] <fo...@ni...> - 2009-04-14 12:24:54
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this is a list of the parameter names that we capture for an animal husbandry protocol (have parallel lists for care protocols for zebrafish, cell culture and embryo culture) we had discussed how to capture these in OBI as part of a protocol. at our end, we consider these to be protocol "variables" which allow us to compare and conglomerate protocols based on similar / different values for key parameters. i will miss the dev call today, and hope to join for PPA where we could continue this discussion. ...jennifer Jennifer Fostel, Ph.D. CEBS Scientific Administrator Global Health Sector, SRA International, Inc Laboratory of Respiratory Biology NIEHS, NIH PO Box 12233 Mail Drop F1-05 111 Alexander Drive Research Triangle Park NC 27709-2233 phone 919 541 5055 fax 919 541 1460 |
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From: Bjoern P. <bp...@li...> - 2009-04-09 04:39:41
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This week's agenda: Agenda this week - requests for SIG paper (if necessary) - continue with vaccine ontology terms (Oliver, can you join?) - work on non placed non-core terms (Philippe, can you join?) |
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From: Bjoern P. <bp...@li...> - 2009-04-02 14:38:31
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Sorry for the late notice. |
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From: Bjoern P. <bp...@li...> - 2009-03-26 14:35:31
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Agenda this week - continue with vaccine ontology terms (Oliver, can you join?) - work on non placed non-core terms - clinical chemistry et al (raised by Jennifer) Bjoern Peters wrote: > Agenda: > - vaccine ontology terms (Oliver, if he can join) > - role interaction (JF, if she can join and necessary) > - work on non placeable non core terms (BP) > + your favorite subject here. > > > ------------------------------------------------------------------------------ > Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are > powering Web 2.0 with engaging, cross-platform capabilities. Quickly and > easily build your RIAs with Flex Builder, the Eclipse(TM)based development > software that enables intelligent coding and step-through debugging. > Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com > _______________________________________________ > Obi-protocol-application-branch mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-protocol-application-branch > -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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From: Bjoern P. <bp...@li...> - 2009-03-19 04:51:23
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Agenda: - vaccine ontology terms (Oliver, if he can join) - role interaction (JF, if she can join and necessary) - work on non placeable non core terms (BP) + your favorite subject here. |
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From: Bjoern P. <bp...@li...> - 2009-03-05 16:57:38
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in a few minutes. Agenda items: - non placeable non core terms (BP) - work on assay template (PRS) - role interaction (JF) -- Bjoern Peters Assistant Member La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters |
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