Re: [Obi-devel] OBI Inconsistent
2 views
Skip to first unread message
Frank Gibson
Jul 3, 2009, 4:37:23 AM7/3/09
to Alan Ruttenberg, Phillip Lord, OBI Developers, obi-bio...@googlegroups.com
Sourceforge seems to be really screwing around with email delivery. Everything works for me and consistency check runs in 16sec and classifies in 100 seconds . The strange obsolete class errors have gone as well, although there are 4 classes under Obsolete that are not in the obsolete file, some in iao, plan and role files.
There are some interesting inferences going on within the Material branch... I think this is largely due to the over-use of role asignments to classes and the need to probably create more defined classes. For example all_cells do not bear the role reagent_role or speciment_role all of the time - which is the statment that is made in the ontology. Either these roles need to be removed or you actually mean to talk about the defined class cell_specimen (cell has_role some specimen_role)
Thanks Melanie for sorting this out
Frank
--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/
There are some interesting inferences going on within the Material branch... I think this is largely due to the over-use of role asignments to classes and the need to probably create more defined classes. For example all_cells do not bear the role reagent_role or speciment_role all of the time - which is the statment that is made in the ontology. Either these roles need to be removed or you actually mean to talk about the defined class cell_specimen (cell has_role some specimen_role)
Thanks Melanie for sorting this out
Frank
On Thu, Jul 2, 2009 at 5:14 PM, Alan Ruttenberg <alanrut...@gmail.com> wrote:
Which flavor of Linux, please? I'll try to run on Linux too. Dmitry
already replied that the earlier problem is fixed
In his svn and we're just negotiating how to get something out
quickly. If the Linux thing can be written up a a report that makes it
easy for him to replicate then he tends to be responsive.
-Alan
On Jul 2, 2009, at 12:06 PM, Phillip Lord
<philli...@newcastle.ac.uk> wrote:
>
>
> I've been trying all of this. It's worth mentioning that there is an
> OS
> dependency. Fact++ on linux crashes. On windows, it seems to 98% and
> has
> stuck there for a while.
>
> Pellet hangs at 1% on linux. Can't get it to do anything at all on
> windows.
>
> Conclusions? Erm, well, none I am afraid.
>
> Phil
>
> Alan Ruttenberg <alanrut...@gmail.com> writes:
>> In my version of P4, with a fresh checked out version of obi
>>
>> svn co https://obi.svn.sourceforge.net/svnroot/obi/trunk/src/
>> ontology obitest
>>
>> And opening branches/obil.owl (obi*l*) I don't get an
>> inconsistency. I
>> did get a reasoner error (bug) using fact++. I don't know if that's
>> intermittent or now.
>>
>> I am downloading fresh copies of protege and will try again.
>>
>> -Alan
>>
>> On Thu, Jul 2, 2009 at 9:34 AM, Alan Ruttenberg<alanrut...@gmail.com
>> > wrote:
>>> No, that is correct. Both properties relate a planned process (the
>>> domain) to anything (the unspecified range).
>>>
>>> -Alan
>>>
>>> On Thu, Jul 2, 2009 at 9:32 AM, James Malone<mal...@ebi.ac.uk>
>>> wrote:
>>>>
>>>> has_specified_input and output have same domain and range.
>>>> Surely that is
>>>> wrong? One should have domain of continuant and range of
>>>> processes and
>>>> other opposite. or have I got that wrong?
>>>>
>>>>
>>>>
>>>> Alan Ruttenberg wrote:
>>>>>
>>>>> I will look at it now.
>>>>> -Alan
>>>>>
>>>>> On Thu, Jul 2, 2009 at 8:54 AM, James Malone<mal...@ebi.ac.uk>
>>>>> wrote:
>>>>>
>>>>>>
>>>>>> P4 also says inconsistent for me. I had a look and it wasn't
>>>>>> obvious
>>>>>> what
>>>>>> was wrong, the problem with these sorts of bugs are that when
>>>>>> everything
>>>>>> is
>>>>>> inconsistent it could be any of the relations, and possibly
>>>>>> just one, but
>>>>>> finding it is a real pain. At this point I'd be happy to
>>>>>> revert. I will
>>>>>> send an email once we're back in play reminding about reasoning
>>>>>> before
>>>>>> committing.
>>>>>>
>>>>>>
>>>>>>
>>>>>> Helen Parkinson wrote:
>>>>>>
>>>>>>>
>>>>>>> At this point is reverting to the last known good an option?
>>>>>>> Might be
>>>>>>> quicker than a fix.
>>>>>>>
>>>>>>> Alan Ruttenberg wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> I don't have p3 installed atm. Can you try p4 and see if you
>>>>>>>> get the
>>>>>>>> same answer?
>>>>>>>> -Alan
>>>>>>>>
>>>>>>>> On Thu, Jul 2, 2009 at 5:04 AM, James
>>>>>>>> Malone<mal...@ebi.ac.uk> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> Hi All,
>>>>>>>>>
>>>>>>>>> I have done a fresh check out of OBI onto both my desktop
>>>>>>>>> and laptop
>>>>>>>>> to
>>>>>>>>> double check and I am getting inconsistency errors with
>>>>>>>>> Pellet in
>>>>>>>>> Protege 3.4. Is anyone else still getting these errors?
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ---
>>>>>>>>> ---
>>>>>>>>> ---
>>>>>>>>> ---
>>>>>>>>> ---
>>>>>>>>> ---
>>>>>>>>> ------------------------------------------------------------
>>>>>>>>> _______________________________________________
>>>>>>>>> Obi-devel mailing list
>>>>>>>>> Obi-...@lists.sourceforge.net
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/obi-devel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ---
>>>>>>>> ---
>>>>>>>> ---
>>>>>>>> ---
>>>>>>>> ---
>>>>>>>> ---------------------------------------------------------------
>>>>>>>> _______________________________________________
>>>>>>>> Obi-devel mailing list
>>>>>>>> Obi-...@lists.sourceforge.net
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/obi-devel
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>>>>>
>>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>
>> ---
>> ---
>> ---
>> ---------------------------------------------------------------------
>> _______________________________________________
>> Obi-devel mailing list
>> Obi-...@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/obi-devel
>>
>>
>
> --
> Phillip Lord, Phone: +44 (0) 191 222 7827
> Lecturer in Bioinformatics, Email: philli...@newcastle.ac.uk
> School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord
> Room 914 Claremont Tower, skype: russet_apples
> Newcastle University, msn: m...@russet.org.uk
> NE1 7RU
------------------------------------------------------------------------------
_______________________________________________
Obi-devel mailing list
Obi-...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obi-devel
--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/
Bjoern Peters
Jul 13, 2009, 8:34:22 PM7/13/09
to obi-bio...@googlegroups.com, Phillip Lord, OBI Developers, Alan Ruttenberg
Frank,
In the call today we went through some of the 'historic' role assignments to materials, and removed several of them. Can you check if the weirdness you noticed are gone, or alternatively point out which invalid role assignments remain?
Thanks
- Bjoern
In the call today we went through some of the 'historic' role assignments to materials, and removed several of them. Can you check if the weirdness you noticed are gone, or alternatively point out which invalid role assignments remain?
Thanks
- Bjoern
Frank Gibson
Jul 14, 2009, 5:45:10 AM7/14/09
to obi-bio...@googlegroups.com, Phillip Lord, OBI Developers, Alan Ruttenberg
Hi,
That is great, the inferred hierarchy is looking alot better now and the _wierdness_ issues I originally noticed now infer correctly under specimen - even enzyme is now inferring as a material!, that is a big improvement. However, there are however a few other things I noticed.
1. Cell culture infers as a chemical solution, due to the fact it has a chemical solution as a part. I don' t think this is correct. I tried creating a culture_medium class but that did not solve it either.
2. The definition of Chimera is that it is an organism, however it does not infer as such. The definition is probably wrong here, Chimera is probably a role, or a defined class composed of two or more different populations of genetically distinct cells. Although more work, I would favor the defined class option and not the role option.
3. The definition of population is to restrictive, it either needs to be renamed organism_population or re-defined to something like "The set of individuals, items, or data from which a statistical sample is taken, to fit better with the new definition of specimen - or both options. The generic population, with subclass organism_population
4. There is a subclass or population called sample_population, this is probably now a synonym of specimen and should be depreciated
5. From the minutes you did mention removing environmental_matter. However, I would remove all envo classes (soil, podzoil) from under material - as per the discussion at the workshop, as envo is likely to be imported somewhere under site, depending on there definition. From the workshop, environment was declared out of scope of OBI - we do not use the sublcasses anywhere in the ontology as it stands.
6. Fragment_derived_from_protein seems a strange class, is this actually just a peptide or amino acid? What is a protein fragment if it is not one of these, what is the example of use?
7. The definition of a polyacrylamide gel is just wrong - I have re-defined this several times, cant find the specific email but can re-define it, if required.
8. Pool_of_specimens does not infer as a collection
9. Should scattered_molecular_aggregate be a defined class?
Cheers
Frank
That is great, the inferred hierarchy is looking alot better now and the _wierdness_ issues I originally noticed now infer correctly under specimen - even enzyme is now inferring as a material!, that is a big improvement. However, there are however a few other things I noticed.
1. Cell culture infers as a chemical solution, due to the fact it has a chemical solution as a part. I don' t think this is correct. I tried creating a culture_medium class but that did not solve it either.
2. The definition of Chimera is that it is an organism, however it does not infer as such. The definition is probably wrong here, Chimera is probably a role, or a defined class composed of two or more different populations of genetically distinct cells. Although more work, I would favor the defined class option and not the role option.
3. The definition of population is to restrictive, it either needs to be renamed organism_population or re-defined to something like "The set of individuals, items, or data from which a statistical sample is taken, to fit better with the new definition of specimen - or both options. The generic population, with subclass organism_population
4. There is a subclass or population called sample_population, this is probably now a synonym of specimen and should be depreciated
5. From the minutes you did mention removing environmental_matter. However, I would remove all envo classes (soil, podzoil) from under material - as per the discussion at the workshop, as envo is likely to be imported somewhere under site, depending on there definition. From the workshop, environment was declared out of scope of OBI - we do not use the sublcasses anywhere in the ontology as it stands.
6. Fragment_derived_from_protein seems a strange class, is this actually just a peptide or amino acid? What is a protein fragment if it is not one of these, what is the example of use?
7. The definition of a polyacrylamide gel is just wrong - I have re-defined this several times, cant find the specific email but can re-define it, if required.
8. Pool_of_specimens does not infer as a collection
9. Should scattered_molecular_aggregate be a defined class?
Cheers
Frank
Frank Gibson
Jul 17, 2009, 6:19:56 AM7/17/09
to obi-bio...@googlegroups.com, Phillip Lord, OBI Developers, Alan Ruttenberg
Hi,
I have added all these issues to the tracker
Frank
I have added all these issues to the tracker
Frank
Philippe Rocca-Serra
Jul 17, 2009, 7:10:00 AM7/17/09
to Frank Gibson, obi-bio...@googlegroups.com, OBI Developers
I have noticed the following:
cDNA library and phage display library are classified under 'recombinant
vector'.
they are asserted rightly under collection.
while it makes sense when looking at the restriction
(is_specified_output_of some 'recombinant vector cloning)
it seems that the label for the defined class is misleading since
libraries are 'collections of recombinant vectors.
so the 'is_a' relation between 'recombinant vector' and 'cDNA library'
sounds ambiguous.
It actually means DNA library has_part 'recombinant_vector'
unless vector is understood broadly.
also the definition for 'recombinant vector' may be refined to included
'propagation' in addition to just 'amplification'
cheers
P
> <mailto:obi-...@lists.sourceforge.net>>,
> obi-bio...@googlegroups.com
> <mailto:obi-bio...@googlegroups.com>
> >>>>>>>> Malone< mal...@ebi.ac.uk <mailto:mal...@ebi.ac.uk> >
> <mailto:Obi-...@lists.sourceforge.net>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/Challenge
> ------------------------------------------------------------------------
Technical Coordinator
www.ebi.ac.uk/net-project
The European Bioinformatics Institute email: ro...@ebi.ac.uk
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
--
cDNA library and phage display library are classified under 'recombinant
vector'.
they are asserted rightly under collection.
while it makes sense when looking at the restriction
(is_specified_output_of some 'recombinant vector cloning)
it seems that the label for the defined class is misleading since
libraries are 'collections of recombinant vectors.
so the 'is_a' relation between 'recombinant vector' and 'cDNA library'
sounds ambiguous.
It actually means DNA library has_part 'recombinant_vector'
unless vector is understood broadly.
also the definition for 'recombinant vector' may be refined to included
'propagation' in addition to just 'amplification'
cheers
P
> obi-bio...@googlegroups.com
> <mailto:obi-bio...@googlegroups.com>
> Sent: Friday, July 3, 2009 1:37:23 AM GMT -08:00 US/Canada Pacific
> Subject: [obi-biomaterial] Re: [Obi-devel] OBI Inconsistent
>
> Sourceforge seems to be really screwing around with email
> delivery. Everything works for me and consistency check runs
> in 16sec and classifies in 100 seconds . The strange obsolete
> class errors have gone as well, although there are 4 classes
> under Obsolete that are not in the obsolete file, some in iao,
> plan and role files.
>
> There are some interesting inferences going on within the
> Material branch... I think this is largely due to the over-use
> of role asignments to classes and the need to probably create
> more defined classes. For example all_cells do not bear the
> role reagent_role or speciment_role all of the time - which is
> the statment that is made in the ontology. Either these roles
> need to be removed or you actually mean to talk about the
> defined class cell_specimen (cell has_role some specimen_role)
>
> Thanks Melanie for sorting this out
>
> Frank
>
>
>
> On Thu, Jul 2, 2009 at 5:14 PM, Alan Ruttenberg <
> alanrut...@gmail.com <mailto:alanrut...@gmail.com> >
> Subject: [obi-biomaterial] Re: [Obi-devel] OBI Inconsistent
>
> Sourceforge seems to be really screwing around with email
> delivery. Everything works for me and consistency check runs
> in 16sec and classifies in 100 seconds . The strange obsolete
> class errors have gone as well, although there are 4 classes
> under Obsolete that are not in the obsolete file, some in iao,
> plan and role files.
>
> There are some interesting inferences going on within the
> Material branch... I think this is largely due to the over-use
> of role asignments to classes and the need to probably create
> more defined classes. For example all_cells do not bear the
> role reagent_role or speciment_role all of the time - which is
> the statment that is made in the ontology. Either these roles
> need to be removed or you actually mean to talk about the
> defined class cell_specimen (cell has_role some specimen_role)
>
> Thanks Melanie for sorting this out
>
> Frank
>
>
>
> On Thu, Jul 2, 2009 at 5:14 PM, Alan Ruttenberg <
> wrote:
>
>
> Which flavor of Linux, please? I'll try to run on Linux too.
> Dmitry
> already replied that the earlier problem is fixed
> In his svn and we're just negotiating how to get something out
> quickly. If the Linux thing can be written up a a report that
> makes it
> easy for him to replicate then he tends to be responsive.
>
> -Alan
>
> On Jul 2, 2009, at 12:06 PM, Phillip Lord
>
>
>
> < philli...@newcastle.ac.uk
>
>
> Which flavor of Linux, please? I'll try to run on Linux too.
> Dmitry
> already replied that the earlier problem is fixed
> In his svn and we're just negotiating how to get something out
> quickly. If the Linux thing can be written up a a report that
> makes it
> easy for him to replicate then he tends to be responsive.
>
> -Alan
>
> On Jul 2, 2009, at 12:06 PM, Phillip Lord
>
>
>
> < philli...@newcastle.ac.uk
> <mailto:philli...@newcastle.ac.uk> > wrote:
>
> >
> >
> > I've been trying all of this. It's worth mentioning that
> there is an
> > OS
> > dependency. Fact++ on linux crashes. On windows, it seems to
> 98% and
> > has
> > stuck there for a while.
> >
> > Pellet hangs at 1% on linux. Can't get it to do anything at
> all on
> > windows.
> >
> > Conclusions? Erm, well, none I am afraid.
> >
> > Phil
> >
> > Alan Ruttenberg < alanrut...@gmail.com
>
> >
> >
> > I've been trying all of this. It's worth mentioning that
> there is an
> > OS
> > dependency. Fact++ on linux crashes. On windows, it seems to
> 98% and
> > has
> > stuck there for a while.
> >
> > Pellet hangs at 1% on linux. Can't get it to do anything at
> all on
> > windows.
> >
> > Conclusions? Erm, well, none I am afraid.
> >
> > Phil
> >
> > Alan Ruttenberg < alanrut...@gmail.com
> <mailto:alanrut...@gmail.com> > writes:
> >> In my version of P4, with a fresh checked out version of obi
> >>
> >> svn co https://obi.svn.sourceforge.net/svnroot/obi/trunk/src/
> >> ontology obitest
> >>
> >> And opening branches/obil.owl (obi*l*) I don't get an
> >> inconsistency. I
> >> did get a reasoner error (bug) using fact++. I don't know
> if that's
> >> intermittent or now.
> >>
> >> I am downloading fresh copies of protege and will try again.
> >>
> >> -Alan
> >>
> >> On Thu, Jul 2, 2009 at 9:34 AM, Alan Ruttenberg<
> alanrut...@gmail.com <mailto:alanrut...@gmail.com>
> >> In my version of P4, with a fresh checked out version of obi
> >>
> >> svn co https://obi.svn.sourceforge.net/svnroot/obi/trunk/src/
> >> ontology obitest
> >>
> >> And opening branches/obil.owl (obi*l*) I don't get an
> >> inconsistency. I
> >> did get a reasoner error (bug) using fact++. I don't know
> if that's
> >> intermittent or now.
> >>
> >> I am downloading fresh copies of protege and will try again.
> >>
> >> -Alan
> >>
> >> On Thu, Jul 2, 2009 at 9:34 AM, Alan Ruttenberg<
> >> > wrote:
> >>> No, that is correct. Both properties relate a planned
> process (the
> >>> domain) to anything (the unspecified range).
> >>>
> >>> -Alan
> >>>
> >>> On Thu, Jul 2, 2009 at 9:32 AM, James Malone<
> mal...@ebi.ac.uk <mailto:mal...@ebi.ac.uk> >
> >>> No, that is correct. Both properties relate a planned
> process (the
> >>> domain) to anything (the unspecified range).
> >>>
> >>> -Alan
> >>>
> >>> On Thu, Jul 2, 2009 at 9:32 AM, James Malone<
> >>> wrote:
> >>>>
> >>>> has_specified_input and output have same domain and range.
> >>>> Surely that is
> >>>> wrong? One should have domain of continuant and range of
> >>>> processes and
> >>>> other opposite. or have I got that wrong?
> >>>>
> >>>>
> >>>>
> >>>> Alan Ruttenberg wrote:
> >>>>>
> >>>>> I will look at it now.
> >>>>> -Alan
> >>>>>
> >>>>> On Thu, Jul 2, 2009 at 8:54 AM, James Malone<
> mal...@ebi.ac.uk <mailto:mal...@ebi.ac.uk> >
> >>>>
> >>>> has_specified_input and output have same domain and range.
> >>>> Surely that is
> >>>> wrong? One should have domain of continuant and range of
> >>>> processes and
> >>>> other opposite. or have I got that wrong?
> >>>>
> >>>>
> >>>>
> >>>> Alan Ruttenberg wrote:
> >>>>>
> >>>>> I will look at it now.
> >>>>> -Alan
> >>>>>
> >>>>> On Thu, Jul 2, 2009 at 8:54 AM, James Malone<
> >>>>>>>>> https://lists.sourceforge.net/lists/listinfo/obi-devel
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>>
> ---------------------------------------------------------------
> >>>>>>>> _______________________________________________
> >>>>>>>> Obi-devel mailing list
> >>>>>>>> Obi-...@lists.sourceforge.net
> <mailto:Obi-...@lists.sourceforge.net>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>> ---
> >>>>>>>>
> ---------------------------------------------------------------
> >>>>>>>> _______________________________________________
> >>>>>>>> Obi-devel mailing list
> >>>>>>>> Obi-...@lists.sourceforge.net
> >>>>>>>> https://lists.sourceforge.net/lists/listinfo/obi-devel
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> 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
> >>>>>>
> >>>>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >>>>
> >>>
> >>
> >> ---
> >> ---
> >> ---
> >>
> ---------------------------------------------------------------------
> >> _______________________________________________
> >> Obi-devel mailing list
> >> Obi-...@lists.sourceforge.net
> <mailto:Obi-...@lists.sourceforge.net>
> >>>>>>>>
> >>>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> 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
> >>>>>>
> >>>>>>
> >>>>
> >>>>
> >>>> --
> >>>> 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
> >>>>
> >>>
> >>
> >> ---
> >> ---
> >> ---
> >>
> ---------------------------------------------------------------------
> >> _______________________________________________
> >> Obi-devel mailing list
> >> Obi-...@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/obi-devel
> >>
> >>
> >
> > --
> > Phillip Lord, Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics, Email:
> philli...@newcastle.ac.uk <mailto:philli...@newcastle.ac.uk>
> >>
> >>
> >
> > --
> > Phillip Lord, Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics, Email:
> > School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower, skype: russet_apples
> > Newcastle University, msn: m...@russet.org.uk
> <mailto:m...@russet.org.uk>
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower, skype: russet_apples
> > Newcastle University, msn: m...@russet.org.uk
> > NE1 7RU
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> <mailto:Obi-...@lists.sourceforge.net>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
>
>
> >
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
> ------------------------------------------------------------------------
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
>
>
> >
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/Challenge
> ------------------------------------------------------------------------
>
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
--
Philippe Rocca-Serra, PhD
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
--
Technical Coordinator
www.ebi.ac.uk/net-project
The European Bioinformatics Institute email: ro...@ebi.ac.uk
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
--
Frank Gibson
Jul 17, 2009, 9:07:16 AM7/17/09
to Philippe Rocca-Serra, obi-bio...@googlegroups.com, OBI Developers
Hi Philippe,
Good spot, we are currently looking at how we defined "vector" and any changes are likely to impact the issues you raise. Can you add your observations to the following tracker item, so we dont miss it and address it as we address "vector"
https://sourceforge.net/tracker/index.php?func=detail&aid=2078795&group_id=177891&atid=886178
Cheers
Frank
Good spot, we are currently looking at how we defined "vector" and any changes are likely to impact the issues you raise. Can you add your observations to the following tracker item, so we dont miss it and address it as we address "vector"
https://sourceforge.net/tracker/index.php?func=detail&aid=2078795&group_id=177891&atid=886178
Cheers
Frank
Reply all
Reply to author
Forward
0 new messages