geneontology-oboedit-working-group Mailing List for [DEPRECATED] Gene Ontology

Thanks!!

On Thu, Dec 3, 2020 at 9:36 AM Dr Midori A. Harris <ma...@ca...> wrote:

> Hi,
>
> On Thu, 3 Dec 2020, Chris Mungall wrote:
>
> > Helloooo... anyone still here?
>
> It would appear that I'm still on this list ... who knew?
>
> > Weren't obo-edit dictionaries great?
>
> Yes. Yes, they were.
>
> > I'd like to try and resuscitate the functionality in robot
> > https://github.com/ontodev/robot/issues/784
> >
> > But I can't find the docs to point developers to. Anyone know if we had
> > this?
>
> The dictionary stuff was part of O-E's verification system, and used four
> files in the oboedit_config/dict/ directory:
>
> - allowedrepeats.dict   allowable repeated words
> - alwayslowercase.dict  for case check
> - periodwords.dict      i.e. not a missing space between sentences
> - standard.dict built-in default dictionary for spell check (I *think*
> it's case sensitive but would have to test it to be sure)
> - user.dict     for anything you want spell check to allow, but don't want
> to add to the default dictionary
>
> The only documentation I know of is what was built into OBO-Edit itself. I
> have a working O-E kicking around, so let me know if it'd be useful for me
> to copy/paste the relevant portions (but it's user-facing documentation,
> so I don't know how much it'll help anyone coding a successor).
>
> cheers,
> Midori
>

Hi,

On Thu, 3 Dec 2020, Chris Mungall wrote:

> Helloooo... anyone still here?

It would appear that I'm still on this list ... who knew?

> Weren't obo-edit dictionaries great?

Yes. Yes, they were.

> I'd like to try and resuscitate the functionality in robot
> https://github.com/ontodev/robot/issues/784
>
> But I can't find the docs to point developers to. Anyone know if we had
> this?

The dictionary stuff was part of O-E's verification system, and used four 
files in the oboedit_config/dict/ directory:

- allowedrepeats.dict	allowable repeated words
- alwayslowercase.dict	for case check
- periodwords.dict	i.e. not a missing space between sentences
- standard.dict	built-in default dictionary for spell check (I *think* 
it's case sensitive but would have to test it to be sure)
- user.dict	for anything you want spell check to allow, but don't want 
to add to the default dictionary

The only documentation I know of is what was built into OBO-Edit itself. I 
have a working O-E kicking around, so let me know if it'd be useful for me 
to copy/paste the relevant portions (but it's user-facing documentation, 
so I don't know how much it'll help anyone coding a successor).

cheers,
Midori

Helloooo... anyone still here?

Weren't obo-edit dictionaries great?

I'd like to try and resuscitate the functionality in robot
https://github.com/ontodev/robot/issues/784

But I can't find the docs to point developers to. Anyone know if we had
this?

If you have opinions about how this is done in Protege, please comment here:
https://github.com/protegeproject/protege/issues/283

Dear OBO-Edit working group,

Many thanks to those of you who have already filled in the Gene Ontology 
(GO) user survey. For those who haven't, a gentle reminder:
Please assist GO by completing a brief survey. The results will tell us 
how to make GO a better tool for your work, and will be used in 
preparation of our grant renewal.

Completed surveys will be eligible for a prize draw.

Thank you in advance for your time,
Paola, for the GO Consortium

Link to survey: https://www.surveymonkey.com/r/CGXWMP5

-- 
Paola Roncaglia, PhD
GO Editorial Office
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 1223 492600
Fax: +44 1223 494468

Dear all,

Please assist the Gene Ontology (GO) project by completing a brief 
survey. The results will help us determine how we can make GO a better 
tool for your work, and will be used in preparation of our grant 
renewal. Completed surveys will be eligible for a prize draw.

Thank you in advance for your time,

Paola, for the GO Consortium

Link to survey: https://www.surveymonkey.com/r/CGXWMP5

-- 
Paola Roncaglia, PhD
GO Editorial Office
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 1223 492600
Fax: +44 1223 494468

Hi All,

The GO has been maintaining a list of Protege plugins that are of 
interest to the GO group as we gradually transition to a more OWL 
oriented workflow, many of you are in the same boat and would find these 
of use:

http://wiki.geneontology.org/index.php/Ontology_editor_plugins

Thanks to Jim Balhoff, Simon Jupp and Heiko Dietze, the core developers, 
and to David OS for pushing us along.

Many of you know how to install plugins in Protege; for everyone else, 
we're hoping to aggregate some of our existing training material into 
something easily digested, so stay tuned, and don't be discouraged if 
you're not sure where to start.

Note that in the list we have an *alpha* version of a new plugin that 
makes it easier to edit OBO-style metadata: synonyms, definitions and 
comments. I know many of you like being on the cutting edge, so we're 
letting you see a sneak peek (I'm already finding it useful), but we're 
not asking for feedback on this plugin just yet, as we know what the 
issues are and will be addressing them in updates over the next month.

Hello,

we have released a new version of OBO-Edit. The new release is version 
2.3.1. It contains only one change:

* Better handling of 'expand_assertion_to' and 'is_class_level' tags.
   These tags (used in typedefs) will no longer be duplicated during an
   OBO-Edit roundtrip (in combination with imports).

We expect no other side effects, and no problems during the upgrade from 
the previous version (2.3).

The release is available from source-forge. Please be aware, on 
source-forge there are sometimes problematic advertisements, which 
pretend to be a download link.

http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.3.1/


regards,

Heiko Dietze

Hello,

This works!

(Anyone who is doing this on a Windows machine should remember to save or output without the Byte-Order Mark, also known as the signature, or strange things will happen to the header and Protégé will cry.)

Many thanks,
Colin.

-----Original Message-----
From: Jim Balhoff [mailto:ba...@gm...] On Behalf Of Jim Balhoff
Sent: 13 January 2014 16:00
To: Colin Batchelor
Cc: Robinson, Peter; Terry Meehan; Chris Mungall; OBO-Edit Working Group; C Smith; Melissa Haendel; Simon Jupp
Subject: Re: [OBO-Edit Working Group] UTF-8? (was RE: Mailing list of transitioning to Protege and OWL for OBO-Edit users)

On Jan 13, 2014, at 5:26 AM, Colin Batchelor <Bat...@rs...> wrote:

> Is there a way of getting non-ASCII characters from the OBO file into the OWL? I ask because I've recently added the Crabbé homologation to RXNO, you see.

This should work if your OBO file is saved with the UTF-8 encoding.

- Jim



____________________________________________
James P. Balhoff, Ph.D.
National Evolutionary Synthesis Center
2024 West Main St., Suite A200
Durham, NC 27705
USA



DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. The Royal Society of Chemistry is a charity, registered in England and Wales, number 207890 - Registered office: Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF

The amount of time spent clicking those boxes is unwieldy. Would love to have a preference not to show them.
Think about all the person hours we'll save!
:-)



On Jan 21, 2014, at 2:14 PM, Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>> wrote:

Many of you use Elk from Protege, and are familiar with the behavior whereby Elk will give warnings like

"GetBottomObjectPropertyNode() not implemented"

And will give you a checkbox not to be warned again - unfortunately the settings are lost when the session ends.

In the absence of a fix in Protege the Elk developers have offered to add a "hidden" option such that you could add something to a preferences file to elect to be never warned. This would be potentially dangerous as you might forget you had that checked this, and subsequently get confused as to why certain inferences weren't showing up. I still think it's worth having - most elk users know they are sacrificing some expressivity for speed (and it's the kind of expressivity that is unfamiliar to many OE users anyway), but I thought I'd check as I'm not really a typical user. What do you think?

Specific details at the end of the thread below

---------- Forwarded message ----------
From: Chris Mungall <cjm...@lb...<mailto:cjm...@lb...>>
Date: Tue, Jan 21, 2014 at 2:01 PM
Subject: Re: Elk plans?
To: elk...@go...<mailto:elk...@go...>



On Tue, Jan 21, 2014 at 9:27 AM, Yevgeny Kazakov <yev...@un...<mailto:yev...@un...>> wrote:
OK, I see.
To prevent using a "process" as a range of "occurs_in", this should
probably work, but what if somebody use "occurs_in" with some new
class, for which you do not have similar disjointness axioms?

yes, the pattern works better for upper-level classes (for which in theory
it should be possible to place all classes in your ontology)

I think a safer solution would be to check externally if, e.g., all
fillers of property restrictions with this property are indeed
sub-classes of the range.
I recall, in Galen ontology there was a similar mechanism using
"sanctions", which basically say that a property can only be used with
some particular classes as domains and ranges (e.g., "part-of" can be
either a relation between anatomical structures, or between, say
ingredients and drugs). Then a classifier was used to check if each
"part-of" was used for one of these valid situations. E.g., if there
was an axiom A part-of B then it was checked whether both A and B are
subclasses of anatomical organs, or wether A is a subclass of
ingredients and B is a subclass of drug, etc. If neither of these was
the case, the editor would return an error.

This is probably the more common scenario for us.


>
>>
>> > 2. coordination with Protege such that we don't get those dialog boxes
>> > all
>> > the time
>>
>> Unfortunately Protege does not currently have a good mechanism for
>> error reporting and cannot recover very well from unsupported
>> exceptions
>> (legally) thrown by OWL API methods. That's why we had to implement
>> all those dialog boxes to let the user know what is going on and what
>> to do about it.
>>
>> An alternative solution would be to silently ignore all problems and
>> implement all unsupported OWL API methods in some default way
>> (essentially producing incorrect results). But we afraid this will
>> cause lots of confusions. Previously we had ELK to only print messages
>> in the console, but not many users run Protege from the command line
>> to see those warning. We had some users mistakingly reporting about
>> missing inferences when we had it in this way.
>>
>> Of course we can easily add a setting which can disable all those
>> dialog messages permanently, but again, it is very easy to forget that
>> all warnings are disabled. That's why, as a compromise, we offer to
>> disable a particular type of warnings within a current session, but if
>> you have a better idea how to approach this problem, please let us
>> know!
>>
>> Which particular dialogs causes the most problems for you?
>
>
> All of them!
>
> Yep, I understand that you need to warn about the missing inferences.
>
> Maybe this is more of a protege request, to remember settings between
> sessions.

The settings can be remembered between the sessions, no problems. ELK
does that already for remembering the number of workers and
incremental reasoning option (specifically in the file
~/.Protege/org.semanticweb.elk/elk.properties). So we could, in
principle, add there an option to disable all warning messages in
Protege -- but this would solve only half of the problem, one has to
do something about non-supported OWL API methods which Protege calls
and gets runtime exceptions.

This results in the red triangle (that everyone ignores)?

But we are also concerned that disabling warnings permanently could
cause some misunderstanding, where the users could expect some results
which are not produced by ELK (the users could easily forget that they
disabled all warnings long time ago).  We could try to add this as a
"hidden" configuration option (set in the file but not in the menu),
and see if that works well for you.

That would be wonderful.

Let me check with some users (I am not a typical Protege user, I do more at the api/command line) but I suspect this would be popular, and people would use it wisely.

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Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library
www.ohsu.edu/library/ontology<http://www.ohsu.edu/library/ontology>
Department of Medical Informatics and Epidemiology
Oregon Health & Science University
ha...@oh...<mailto:ha...@oh...>
skype: melissa.haendel
503-407-5970

Many of you use Elk from Protege, and are familiar with the behavior
whereby Elk will give warnings like

"GetBottomObjectPropertyNode() not implemented"

And will give you a checkbox not to be warned again - unfortunately the
settings are lost when the session ends.

In the absence of a fix in Protege the Elk developers have offered to add a
"hidden" option such that you could add something to a preferences file to
elect to be never warned. This would be potentially dangerous as you might
forget you had that checked this, and subsequently get confused as to why
certain inferences weren't showing up. I still think it's worth having -
most elk users know they are sacrificing some expressivity for speed (and
it's the kind of expressivity that is unfamiliar to many OE users anyway),
but I thought I'd check as I'm not really a typical user. What do you think?

Specific details at the end of the thread below

---------- Forwarded message ----------
From: Chris Mungall <cjm...@lb...>
Date: Tue, Jan 21, 2014 at 2:01 PM
Subject: Re: Elk plans?
To: elk...@go...



On Tue, Jan 21, 2014 at 9:27 AM, Yevgeny Kazakov <yev...@un...
> wrote:

> OK, I see.
> To prevent using a "process" as a range of "occurs_in", this should
> probably work, but what if somebody use "occurs_in" with some new
> class, for which you do not have similar disjointness axioms?
>

yes, the pattern works better for upper-level classes (for which in theory
it should be possible to place all classes in your ontology)


> I think a safer solution would be to check externally if, e.g., all
> fillers of property restrictions with this property are indeed
> sub-classes of the range.
> I recall, in Galen ontology there was a similar mechanism using
> "sanctions", which basically say that a property can only be used with
> some particular classes as domains and ranges (e.g., "part-of" can be
> either a relation between anatomical structures, or between, say
> ingredients and drugs). Then a classifier was used to check if each
> "part-of" was used for one of these valid situations. E.g., if there
> was an axiom A part-of B then it was checked whether both A and B are
> subclasses of anatomical organs, or wether A is a subclass of
> ingredients and B is a subclass of drug, etc. If neither of these was
> the case, the editor would return an error.
>

This is probably the more common scenario for us.


>
> >
> >>
> >> > 2. coordination with Protege such that we don't get those dialog boxes
> >> > all
> >> > the time
> >>
> >> Unfortunately Protege does not currently have a good mechanism for
> >> error reporting and cannot recover very well from unsupported
> >> exceptions
> >> (legally) thrown by OWL API methods. That's why we had to implement
> >> all those dialog boxes to let the user know what is going on and what
> >> to do about it.
> >>
> >> An alternative solution would be to silently ignore all problems and
> >> implement all unsupported OWL API methods in some default way
> >> (essentially producing incorrect results). But we afraid this will
> >> cause lots of confusions. Previously we had ELK to only print messages
> >> in the console, but not many users run Protege from the command line
> >> to see those warning. We had some users mistakingly reporting about
> >> missing inferences when we had it in this way.
> >>
> >> Of course we can easily add a setting which can disable all those
> >> dialog messages permanently, but again, it is very easy to forget that
> >> all warnings are disabled. That's why, as a compromise, we offer to
> >> disable a particular type of warnings within a current session, but if
> >> you have a better idea how to approach this problem, please let us
> >> know!
> >>
> >> Which particular dialogs causes the most problems for you?
> >
> >
> > All of them!
> >
> > Yep, I understand that you need to warn about the missing inferences.
> >
> > Maybe this is more of a protege request, to remember settings between
> > sessions.
>
> The settings can be remembered between the sessions, no problems. ELK
> does that already for remembering the number of workers and
> incremental reasoning option (specifically in the file
> ~/.Protege/org.semanticweb.elk/elk.properties). So we could, in
> principle, add there an option to disable all warning messages in
> Protege -- but this would solve only half of the problem, one has to
> do something about non-supported OWL API methods which Protege calls
> and gets runtime exceptions.
>

This results in the red triangle (that everyone ignores)?


>  But we are also concerned that disabling warnings permanently could
> cause some misunderstanding, where the users could expect some results
> which are not produced by ELK (the users could easily forget that they
> disabled all warnings long time ago).  We could try to add this as a
> "hidden" configuration option (set in the file but not in the menu),
> and see if that works well for you.
>

That would be wonderful.

Let me check with some users (I am not a typical Protege user, I do more at
the api/command line) but I suspect this would be popular, and people would
use it wisely.

+1 for keeping the same list

Ramona

-------------------------------------
Ramona Walls
New York Botanical Garden
2900 Southern Blvd.
Bronx, NY 10458
(516)885-8005
________________________________
From: David Osumi-Sutherland [dj...@ge...]
Sent: Friday, January 10, 2014 12:08 PM
To: Terry Meehan
Cc: Peter Robinson; Simon Jupp; Chris Mungall; C Smith; melissa haendel; OBO-Edit Working Group
Subject: Re: [OBO-Edit Working Group] Mailing list of transitioning to Protege and OWL for OBO-Edit users

On 10 Jan 2014, at 16:49, Terry Meehan <tm...@eb...<mailto:tm...@eb...>> wrote:

Repurposing the list is fine for me.

Me too.  Makes sense as a way to keep major OE users informed of progress and get their input.


Terry
On 10/01/2014 16:33, Chris Mungall wrote:
Many people on this list are somewhere on the path to transitioning to OWL and facing similar issues: particularly needing OE-like features in Protege.

Should we repurpose this list, or create a new dedicated one?




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--
Terry Meehan, Ph.D.
Project Co-Leader, Mouse Informatics
tm...@eb...<mailto:tm...@eb...>
+44(0)1223 492 591
European Molecular Biology Laboratory-
European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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Everyone should be able to read/comment/write:

https://docs.google.com/document/d/17tph3jwrDGEaa7DyYPOK8HCi2dCDdJxi3VrTWNQpbqc/edit#

(apologies for all the OWL terminology, hopefully it should be reasonably
clear)

I have made the assumption that certain behaviors of the OE text editor
(e.g. having each annotation property be in its own tab) are _not_
desirable.

Once we're reasonable happy with the spec we'll figure out what the plan
for development is - I don't think it should be too hard to have the core
features implemented as a plugin.

On Jan 13, 2014, at 5:26 AM, Colin Batchelor <Bat...@rs...> wrote:

> Is there a way of getting non-ASCII characters from the OBO file into the OWL? I ask because I've recently added the Crabbé homologation to RXNO, you see.

This should work if your OBO file is saved with the UTF-8 encoding.

- Jim



____________________________________________
James P. Balhoff, Ph.D.
National Evolutionary Synthesis Center
2024 West Main St., Suite A200
Durham, NC 27705
USA

Hello,

+1 from me - I have migrated machines a few times, have a new text editor/OORT/Protégé workflow and have mislaid OBO-Edit along the way.

Is there a way of getting non-ASCII characters from the OBO file into the OWL? I ask because I've recently added the Crabbé homologation to RXNO, you see.

Best wishes,
Colin.

-----Original Message-----
From: Robinson, Peter [mailto:pet...@ch...] 
Sent: 10 January 2014 19:47
To: Terry Meehan; Chris Mungall; OBO-Edit Working Group
Cc: C Smith; melissa haendel; Simon Jupp
Subject: Re: [OBO-Edit Working Group] Mailing list of transitioning to Protege and OWL for OBO-Edit users

I would also vote for sticking to the same list -Peter

Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin Institut für Medizinische Genetik und Humangenetik Charité - Universitätsmedizin Berlin Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
pet...@ch...
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson ________________________________________
Von: Terry Meehan [tm...@eb...]
Gesendet: Freitag, 10. Januar 2014 17:49
An: Chris Mungall; OBO-Edit Working Group
Cc: Robinson, Peter; C Smith; melissa haendel; Simon Jupp
Betreff: Re: [OBO-Edit Working Group] Mailing list of transitioning to Protege and OWL for OBO-Edit users

Repurposing the list is fine for me.

Terry
On 10/01/2014 16:33, Chris Mungall wrote:
Many people on this list are somewhere on the path to transitioning to OWL and facing similar issues: particularly needing OE-like features in Protege.

Should we repurpose this list, or create a new dedicated one?




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_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group




--
Terry Meehan, Ph.D.
Project Co-Leader, Mouse Informatics
tm...@eb...<mailto:tm...@eb...>
+44(0)1223 492 591
European Molecular Biology Laboratory-
European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.


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_______________________________________________
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DISCLAIMER:

This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening. The Royal Society of Chemistry is a charity, registered in England and Wales, number 207890 - Registered office: Thomas Graham House, Science Park, Milton Road, Cambridge CB4 0WF

I would also vote for sticking to the same list
-Peter

Dr. med. Peter N. Robinson, MSc.
Professor of Medical Genomics
Professor in the Bioinformatics Division of the Department of Mathematics and Computer Science of the Freie Universität Berlin
Institut für Medizinische Genetik und Humangenetik
Charité - Universitätsmedizin Berlin
Augustenburger Platz 1
13353 Berlin
Germany
+4930 450566006
Mobile: 0160 93769872
pet...@ch...
http://compbio.charite.de
http://www.human-phenotype-ontology.org
Introduction to Bio-Ontologies: http://www.crcpress.com/product/isbn/9781439836651
I have learned from my mistakes, and I am sure I can repeat them exactly
ORCID ID:http://orcid.org/0000-0002-0736-9199
Scopus Author ID 7403719646
Appointment request: http://doodle.com/pnrobinson
________________________________________
Von: Terry Meehan [tm...@eb...]
Gesendet: Freitag, 10. Januar 2014 17:49
An: Chris Mungall; OBO-Edit Working Group
Cc: Robinson, Peter; C Smith; melissa haendel; Simon Jupp
Betreff: Re: [OBO-Edit Working Group] Mailing list of transitioning to Protege and OWL for OBO-Edit users

Repurposing the list is fine for me.

Terry
On 10/01/2014 16:33, Chris Mungall wrote:
Many people on this list are somewhere on the path to transitioning to OWL and facing similar issues: particularly needing OE-like features in Protege.

Should we repurpose this list, or create a new dedicated one?




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--
Terry Meehan, Ph.D.
Project Co-Leader, Mouse Informatics
tm...@eb...<mailto:tm...@eb...>
+44(0)1223 492 591
European Molecular Biology Laboratory-
European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

On 10 Jan 2014, at 16:49, Terry Meehan <tm...@eb...> wrote:

> Repurposing the list is fine for me.

Me too.  Makes sense as a way to keep major OE users informed of progress and get their input.

> 
> Terry
> On 10/01/2014 16:33, Chris Mungall wrote:
>> Many people on this list are somewhere on the path to transitioning to OWL and facing similar issues: particularly needing OE-like features in Protege.
>> 
>> Should we repurpose this list, or create a new dedicated one?
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
>> Learn Why More Businesses Are Choosing CenturyLink Cloud For
>> Critical Workloads, Development Environments & Everything In Between.
>> Get a Quote or Start a Free Trial Today. 
>> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>> 
>> 
>> _______________________________________________
>> Geneontology-oboedit-working-group mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group
> 
> 
> -- 
> Terry Meehan, Ph.D.
> Project Co-Leader, Mouse Informatics
> tm...@eb...
> +44(0)1223 492 591
> European Molecular Biology Laboratory- 
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. 
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today. 
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk_______________________________________________
> Geneontology-oboedit-working-group mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group

Repurposing the list is fine for me.

Terry
On 10/01/2014 16:33, Chris Mungall wrote:
> Many people on this list are somewhere on the path to transitioning to 
> OWL and facing similar issues: particularly needing OE-like features 
> in Protege.
>
> Should we repurpose this list, or create a new dedicated one?
>
>
>
> ------------------------------------------------------------------------------
> CenturyLink Cloud: The Leader in Enterprise Cloud Services.
> Learn Why More Businesses Are Choosing CenturyLink Cloud For
> Critical Workloads, Development Environments & Everything In Between.
> Get a Quote or Start a Free Trial Today.
> http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> Geneontology-oboedit-working-group mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group


-- 
Terry Meehan, Ph.D.
Project Co-Leader, Mouse Informatics
tm...@eb...
+44(0)1223 492 591
European Molecular Biology Laboratory-
European Bioinformatics Institute,
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

Many people on this list are somewhere on the path to transitioning to OWL
and facing similar issues: particularly needing OE-like features in Protege.

Should we repurpose this list, or create a new dedicated one?

Hello,

we are pleased to announce the release of OBO-Edit 2.3. The files are 
available on SourceForge, here:
http://sourceforge.net/projects/geneontology/


Overview of the new features and bugfixes in OBO-Edit 2.3

New features:
- Better handling of import statements in OBO, preserve import headers
   during loading of ontologies
- Allow redirects of import statements using a catalog file. The
   catalog file must be in the same folder as the ontology and be named
   'oboedit.catalog'. It uses a simple pair value format with whitespace
   as delimiters and '#' as comment symbol.
- Add option to filter and render links with a trailing qualifier value
   of: is_inferred="true"
- Add option to advanced file save dialog: Checkbox for include xref
   descriptions for def and synonym tags (unchecked by default)
   [geneontology-Bugs-3366931]
- Add an option to use extra (and external) dictionary files
- Updated obo2owl/owl2obo library

BugFixes:
- Term merging, fixed missing synonym types
   http://sourceforge.net/p/geneontology/bugs/1191/
- Term merging, fixed missing subset tags
   http://sourceforge.net/p/geneontology/bugs/1187/
- Term merging, fixed missing Def xrefs
- Compatibility issues with Java 7
   [geneontology-Bugs-3495346], [geneontology-Bugs-3523730],
   [geneontology-Bugs-3534554]
- Multiple versions of the obo2owl library in the OBO-Edit installer


We expect no incompatibilities in upgrading from existing OBO-Edit 2.2 
installations to the latest release.

regards,

Heiko Dietze

Hi Heiko,

Yes, that did the trick. It installs fine. Thank you very much.

Cheer,
Marcus

On 11/5/13, 3:54 PM, "Heiko Dietze" <hd...@lb...> wrote:

>Hello Marcus,
>
>thank you for your feedback. I have checked the installer file from
>Sourceforge and it works normal. The problem is most likely due to the
>security settings of MacOS (10.8 and newer). Apple tries to enforce that
>all applications are digitally signed and/or are installed via the app
>store. Neither is an option for OBO-Edit.
>
>You can find a detailed explanation and how to get around it here:
>http://www.support4world.com/apple/disabling-mac-appstore-to-install-unsig
>ned-application
>
>regards,
>
>Heiko Dietze
>
>On 11/5/13 12:23 PM, Chibucos, Marcus wrote:
>> Not sure if others are experiencing this, but when I tried to run the
>>OE 2.3-b7 installer on OS X 10.9 on a MacBook Pro an error warned me
>>that the "OBO-Edit2 Installer" is damaged and can't be opened. I
>>downloaded again onto an entirely different computer (a MacBook Air,
>>same OS), but got the same error when I tried to run the installer. Not
>>sure if it's something with the download site, corruption during
>>download, a bad package itself, or something to do with my OS. Can
>>someone verify that they have gotten it running on a Mac running
>>Mavericks?
>>
>> Best,
>> Marcus
>> ________________________________________
>> From: Heiko Dietze [hd...@lb...]
>> Sent: Monday, November 04, 2013 3:56 PM
>> To: OBO-Edit Working Group; GO Ontology Editors
>> Subject: [OBO-Edit Working Group] OBO-Edit 2.3-beta7 available
>>
>> Hello,
>>
>> there is a new beta release for OBO-Edit available (OE 2.3-b7).
>> We have modified the behavior of OBO-Edit, that it now preserves import
>> statements.
>> As an additional feature for dealing with imports, we have added the
>> option to redirects of import statements using an catalog file. The
>> catalog file must be in the same folder as the ontology and be named
>> 'oboedit.catalog'. It uses a simple pair value format with whitespace as
>> delimiters and '#' as comment symbol.
>>
>> The release is available in the usual place on the GeneoOntology
>> SourceForge site: http://sourceforge.net/projects/geneontology
>>
>> regards,
>>
>> Heiko Dietze
>>
>> 
>>-------------------------------------------------------------------------
>>--
>> ---
>> Android is increasing in popularity, but the open development platform
>>that
>> developers love is also attractive to malware creators. Download this
>>white
>> paper to learn more about secure code signing practices that can help
>>keep
>> Android apps secure.
>> 
>>http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clkt
>>rk
>> _______________________________________________
>> Geneontology-oboedit-working-group mailing list
>> Gen...@li...
>> 
>>https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working
>>-g
>> roup
>>
>>

Hello Marcus,

thank you for your feedback. I have checked the installer file from 
Sourceforge and it works normal. The problem is most likely due to the 
security settings of MacOS (10.8 and newer). Apple tries to enforce that 
all applications are digitally signed and/or are installed via the app 
store. Neither is an option for OBO-Edit.

You can find a detailed explanation and how to get around it here:
http://www.support4world.com/apple/disabling-mac-appstore-to-install-unsigned-application

regards,

Heiko Dietze

On 11/5/13 12:23 PM, Chibucos, Marcus wrote:
> Not sure if others are experiencing this, but when I tried to run the OE 2.3-b7 installer on OS X 10.9 on a MacBook Pro an error warned me that the "OBO-Edit2 Installer" is damaged and can't be opened. I downloaded again onto an entirely different computer (a MacBook Air, same OS), but got the same error when I tried to run the installer. Not sure if it's something with the download site, corruption during download, a bad package itself, or something to do with my OS. Can someone verify that they have gotten it running on a Mac running Mavericks?
>
> Best,
> Marcus
> ________________________________________
> From: Heiko Dietze [hd...@lb...]
> Sent: Monday, November 04, 2013 3:56 PM
> To: OBO-Edit Working Group; GO Ontology Editors
> Subject: [OBO-Edit Working Group] OBO-Edit 2.3-beta7 available
>
> Hello,
>
> there is a new beta release for OBO-Edit available (OE 2.3-b7).
> We have modified the behavior of OBO-Edit, that it now preserves import
> statements.
> As an additional feature for dealing with imports, we have added the
> option to redirects of import statements using an catalog file. The
> catalog file must be in the same folder as the ontology and be named
> 'oboedit.catalog'. It uses a simple pair value format with whitespace as
> delimiters and '#' as comment symbol.
>
> The release is available in the usual place on the GeneoOntology
> SourceForge site: http://sourceforge.net/projects/geneontology
>
> regards,
>
> Heiko Dietze
>
> ---------------------------------------------------------------------------
> ---
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> _______________________________________________
> Geneontology-oboedit-working-group mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-g
> roup
>
>

Not sure if others are experiencing this, but when I tried to run the OE 2.3-b7 installer on OS X 10.9 on a MacBook Pro an error warned me that the "OBO-Edit2 Installer" is damaged and can't be opened. I downloaded again onto an entirely different computer (a MacBook Air, same OS), but got the same error when I tried to run the installer. Not sure if it's something with the download site, corruption during download, a bad package itself, or something to do with my OS. Can someone verify that they have gotten it running on a Mac running Mavericks?

Best,
Marcus
________________________________________
From: Heiko Dietze [hd...@lb...]
Sent: Monday, November 04, 2013 3:56 PM
To: OBO-Edit Working Group; GO Ontology Editors
Subject: [OBO-Edit Working Group] OBO-Edit 2.3-beta7 available

Hello,

there is a new beta release for OBO-Edit available (OE 2.3-b7).
We have modified the behavior of OBO-Edit, that it now preserves import
statements.
As an additional feature for dealing with imports, we have added the
option to redirects of import statements using an catalog file. The
catalog file must be in the same folder as the ontology and be named
'oboedit.catalog'. It uses a simple pair value format with whitespace as
delimiters and '#' as comment symbol.

The release is available in the usual place on the GeneoOntology
SourceForge site: http://sourceforge.net/projects/geneontology

regards,

Heiko Dietze

---------------------------------------------------------------------------
---
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
_______________________________________________
Geneontology-oboedit-working-group mailing list
Gen...@li...
https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-g
roup

Hello,

there is a new beta release for OBO-Edit available (OE 2.3-b7).
We have modified the behavior of OBO-Edit, that it now preserves import 
statements.
As an additional feature for dealing with imports, we have added the 
option to redirects of import statements using an catalog file. The 
catalog file must be in the same folder as the ontology and be named 
'oboedit.catalog'. It uses a simple pair value format with whitespace as 
delimiters and '#' as comment symbol.

The release is available in the usual place on the GeneoOntology 
SourceForge site: http://sourceforge.net/projects/geneontology

regards,

Heiko Dietze

You're right. User error on my part, thanks!


On Wed, Oct 16, 2013 at 6:43 PM, Wasila Dahdul <wd...@gm...> wrote:

> It works for me using OE 2.3-beta 5, with the same save options you have.
>  I tested on this file (filter on namespace teleost_anatomy):
> https://svn.code.sf.net/p/phenoscape/code/trunk/vocab/teleost_anatomy_VAO_edit.obo
>
> By the way, I don't recall ever losing dangling links when saving.
>
> Sorry I can't provide more help!
> Wasila
>
> On Oct 16, 2013, at 9:02 PM, Chris Mungall wrote:
>
> I should know the answer to this, shouldn't I?
>
> ontology A includes links to ontology B. The links live in ontology A.
>
> I'm trying to make a save filter such that IDs in A get saved in A.obo,
> along with dangling links to B.
>
> I have "filter terms" and "allow dangling parents" selected, yet the save
> always drops the dangling links from A.obo (which is particularly
> calamitous if these are intersection_of / equivalence axioms)
>
> I'm fairly sure this used to work. It's been a while since I delved into
> the code here, and am loathe to make changes at this stage.
>
> Midori and Wasila, I think you were the pioneers of this option. Did you
> have a setup that works?
>
>
>
>