NCBO Wiki - User contributions [en]

Phenote:Main Page

2008-01-06T19:36:32Z

Nicolew: /* Phenote Working Group */

==Phenote - A biomedical annotation tool using ontologies==

This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.

=== What is Phenote? ===

Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.

This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]

For more information, please visit the website at [http://www.phenote.org phenote.org]

=== Who should be interested in Phenote? ===

Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.

===Request tracker===

You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications

* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]

===Mailing List===

The OBO Phenote list is for discussion of Phenote software, announcements, etc.

You can subscribe or browse the archives here:

* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]

===Phenote Developers Group===
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.

===Phenote Working Group===
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, February 7, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.

The goals of the Phenote Users Group are to:
# drive the development of the software by prioritizing features
# test new beta releases; reporting, and prioritizing bug fixes
# sign off on new releases for the general public
# contributing to documentation

====Joining the Working Group WebEx Chat====
Webex Instructions:

Topic: NCBO: Monthly Phenote Users Meeting
Date: The 1st Thursday of every 1 month
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)
Meeting Number: 926 281 546
Meeting Password: phenote
-------------------------------------------------------
To join the online meeting
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e
2. Enter your name and email address.
3. Enter the meeting password: phenote
4. Click "Join Now".

*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php

*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.

====Members====
A dedicated group of users are part of this evaluation team. They include:

*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon
*Neuroscholar: Gully Burns; USC
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University
*BIRN: Maryann Martone; UCSD
*Wormbase: Karen Yook, Gary S; CalTech
*Xenbase: Erik Segerdell; University of Calgary
*OME: Will Moore; University of Dundee

If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]

Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.

====Phenote:Agendas & Transcripts====
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]

* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]

* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]

* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]

* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]

* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting

===Sandbox===

*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]

===ProtocolEditor and matrix view for BIRN===
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.
Here is a nice video of his protocol editor:

http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov

The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:

Dendrite length microns (user enters integer or float)
Brain-cell color (user enters from drop down list of colors from pato)
Dendrite shape warped (user checks true/false checkbox)

To generalize there are 3 different types of Observables: measurements (with units), Attribute with value pick list, and presence(true/false) of a Value. All require an Entity.

For a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.

In a matrix view the columns would be Observables. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.

You can still view the traditional table view of 1 row per phenotype (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.

Another question is how would BIRN like to take advantage of the protocol editor & matrix.
Would this be helpful for literature curation?
Can this be utilized in the context of Smart Atlas? or JINX?
Or would this be used as an experiment/image annotation tool in its own right?

Phenote:Main Page

2008-01-06T19:34:15Z

Nicolew: /* Members */

==Phenote - A biomedical annotation tool using ontologies==

This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.

=== What is Phenote? ===

Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.

This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]

For more information, please visit the website at [http://www.phenote.org phenote.org]

=== Who should be interested in Phenote? ===

Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.

===Request tracker===

You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications

* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]

===Mailing List===

The OBO Phenote list is for discussion of Phenote software, announcements, etc.

You can subscribe or browse the archives here:

* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]

===Phenote Developers Group===
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.

===Phenote Working Group===
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, January 3, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.

The goals of the Phenote Users Group are to:
# drive the development of the software by prioritizing features
# test new beta releases; reporting, and prioritizing bug fixes
# sign off on new releases for the general public
# contributing to documentation

====Joining the Working Group WebEx Chat====
Webex Instructions:

Topic: NCBO: Monthly Phenote Users Meeting
Date: The 1st Thursday of every 1 month
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)
Meeting Number: 926 281 546
Meeting Password: phenote
-------------------------------------------------------
To join the online meeting
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e
2. Enter your name and email address.
3. Enter the meeting password: phenote
4. Click "Join Now".

*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php

*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.

====Members====
A dedicated group of users are part of this evaluation team. They include:

*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon
*Neuroscholar: Gully Burns; USC
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University
*BIRN: Maryann Martone; UCSD
*Wormbase: Karen Yook, Gary S; CalTech
*Xenbase: Erik Segerdell; University of Calgary
*OME: Will Moore; University of Dundee

If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]

Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.

====Phenote:Agendas & Transcripts====
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]

* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]

* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]

* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]

* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]

* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting

===Sandbox===

*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]

===ProtocolEditor and matrix view for BIRN===
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.
Here is a nice video of his protocol editor:

http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov

The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:

Dendrite length microns (user enters integer or float)
Brain-cell color (user enters from drop down list of colors from pato)
Dendrite shape warped (user checks true/false checkbox)

To generalize there are 3 different types of Observables: measurements (with units), Attribute with value pick list, and presence(true/false) of a Value. All require an Entity.

For a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.

In a matrix view the columns would be Observables. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.

You can still view the traditional table view of 1 row per phenotype (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.

Another question is how would BIRN like to take advantage of the protocol editor & matrix.
Would this be helpful for literature curation?
Can this be utilized in the context of Smart Atlas? or JINX?
Or would this be used as an experiment/image annotation tool in its own right?

Phenote:Main Page

2008-01-03T00:40:50Z

Nicolew: /* Phenote Working Group */

==Phenote - A biomedical annotation tool using ontologies==

This wiki page currently serves as the public Phenote project page for posting of materials related to its development. In particular, this will be the site used for announcement and posting of working group agendas and reports/transcripts.

=== What is Phenote? ===

Phenote is a software application and open-source toolkit to facilitate annotation of biomedical data using ontologies. It is being driven by its development as a phenotype annotation tool, but is generalizable to any tool to be used for annotation using ontologies.

This is being developed by the [http://berkeleybop.org Core 2] group with the [http://www.bioontology.org National Center for Biomedical Ontology.]

For more information, please visit the website at [http://www.phenote.org phenote.org]

=== Who should be interested in Phenote? ===

Anyone doing annotation using ontologies. Specifically, anyone doing phenotype annotation such as biocurators affiliated with model organism databases, biological/medical image analysts and ontology developers.

===Request tracker===

You can use the tracker (currently hosted on sourceforge) to request new items or suggest modifications

* [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote Request tracker on sourceforge]

===Mailing List===

The OBO Phenote list is for discussion of Phenote software, announcements, etc.

You can subscribe or browse the archives here:

* [https://lists.sourceforge.net/lists/listinfo/obo-phenote OBO-Phenote Mail List]

===Phenote Developers Group===
The Phenote Developers Group has regularly scheduled meetings on the ''second and fourth Tuesdays of each month, 10:30am (Pacific time)''. If you are currently developing Phenote code or are interested in contributing, please join us for our next meeting on '''Tuesday, August 14th, 2007'''. These will be conducted by phone by dialing in to 877.208.9784. Please shoot me an email for the passcode.

===Phenote Working Group===
The Phenote User group has a regularly scheduled meeting on the ''first Thursday of each month, 8:30am (Pacific time)''. Please join us for our next chat on '''Thursday, January 3, 2008'''. These will be conducted by WebEx, although an occasional live telephone conference might be in order.

The goals of the Phenote Users Group are to:
# drive the development of the software by prioritizing features
# test new beta releases; reporting, and prioritizing bug fixes
# sign off on new releases for the general public
# contributing to documentation

====Joining the Working Group WebEx Chat====
Webex Instructions:

Topic: NCBO: Monthly Phenote Users Meeting
Date: The 1st Thursday of every 1 month
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco)
Meeting Number: 926 281 546
Meeting Password: phenote
-------------------------------------------------------
To join the online meeting
-------------------------------------------------------
1. Go to https://stanford.webex.com/stanford/j.php?ED=96176737&UID=1007605127&PW=c0245958041d0b180e
2. Enter your name and email address.
3. Enter the meeting password: phenote
4. Click "Join Now".

*If you have never run Webex on your computer or it has been a while since you have, I suggest clicking the link below to run any necessary software updates well ahead of the meeting time: https://stanford.webex.com/stanford/meetingcenter/mcsetup.php

*Other meetings: To join in the IRC chat, you will need to use an [http://www.phenote/org/irc_clients.shtml IRC client] and join the irc.sf.net #phenote channel. Alternatively, you can utilize the Phenote IRC applet through your browser by visiting [http://www.phenote.org/irc_chat http://www.phenote.org/irc_chat]. Please visit this webpage for further instructions.

====Members====
A dedicated group of users are part of this evaluation team. They include:

*NCBO: Mark Gibson, Nicole Washington (Developers); Lawrence Berkeley National Labs
*Flybase: Michael Ashburner, David Sutherland; University of Cambridge
*Zfin: Amy Singer, Yvonne Bradford, Melissa Haendel; University of Oregon
*Neuroscholar: Gully Burns, USC
*NESCent: Jim Balhoff, Hilmar Lapp; Duke University
*Dictybase:
*BIRN:
*Wormbase: Gary S; CalTech
*GO:
*Xenbase: Erik Segerdell, University of Calgary

If you'd like to join this group, please add yourself to this list and contact [[mailto:NLWashington@lbl.gov Nicole Washington]]

Most communications for this group (including announcements of upcoming meetings) will be conducted on the obo-phenote mailing list.

====Phenote:Agendas & Transcripts====
* [[Phenote:Agenda: October 2, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_webex_100207.html Transcripts]]

* [[Phenote:Agenda: August 7, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_080707.html Transcripts]]

* [[Phenote:Minutes: July 3, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_070307.html Transcripts]]

* [[Phenote:Minutes: June 5, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_060507.html Transcripts]]

* [[Phenote:Minutes: May 1, 2007]]; [[http://www.phenote.org/irc_chat/transcripts/PWG_irc_050107.html Transcripts]]

* [[Phenote:Minutes: April 10, 2007]] - inaugural meeting

===Sandbox===

*Annotation Standards: A collection for OMIM annotation. [[OMIM Annotation Standards]]
*Annotation Standards: A collection from various phenotype annotation resources [[MOD Phenotype Annotation Standards]]

===ProtocolEditor and matrix view for BIRN===
We are currently collaborating with Will Moore at the OME at Dundee, Scotland on integrating his ProtocolEditor with Phenote.
Here is a nice video of his protocol editor:

http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov

The idea is that one defines "Observables" in the ProtocolEditor in addition to everything about the experiment. The observables will be items one wants to record using Phenote. Some examples (from a non-biologist) might be:

Dendrite length microns (user enters integer or float)
Brain-cell color (user enters from drop down list of colors from pato)
Dendrite shape warped (user checks true/false checkbox)

To generalize there are 3 different types of Observables: measurements (with units), Attribute with value pick list, and presence(true/false) of a Value. All require an Entity.

For a pato attribute, all of the values below the attribute will be available as a pick list, so color would show all of the color values listed in pato.

In a matrix view the columns would be Observables. A row would be something you were making these statements about, like an image (with an image ID). So a row of the matrix would then contain multiple phenotype statements, capturing all of the phenotype information you want to make about a particular image. The matrix allows you to rapidly go through and characterize images, and allows you to see in one line all the data for an image.

You can still view the traditional table view of 1 row per phenotype (with image ID repeated). In this view one can add more information about a particular phenotype, like free text description and such. It should also be possible to add additional Phentoypes that are observed for any image, using one row per Phenotype as usual. Upon returning to the matrix view, these could be displayed in "Additional Phenotype" columns (EQ column pairs - an additional pair of columns for each additional Phenotype), thereby maintaining one image per row.

Another question is how would BIRN like to take advantage of the protocol editor & matrix.
Would this be helpful for literature curation?
Can this be utilized in the context of Smart Atlas? or JINX?
Or would this be used as an experiment/image annotation tool in its own right?

Phenote:Main Page

2007-11-27T17:07:26Z

Nicolew: /* Phenote Working Group */

Phenote:Main Page

2007-11-16T01:38:58Z

Nicolew: /* Sandbox */

OMIM Annotation Standards

2007-11-05T22:53:34Z

Nicolew: /* Basic Rules */

This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax.

==Basic Rules==
# Use the ncbo 'config'. This will include automatic updates to the latest ontologies from SF.
# No use of MP, though it can be used to look for good cross-products
# Use the same style for gene ids. ie. OMIM:601653.0005 (database:identifier dot allele designation)
# no postcomposition using GO:Biological_Process with a continuant
# limit the post-comp relation to part_of. we can discuss this- but this is what we do at zfin, so at least the zebrafish data is biased in this way already
# If its known that a process is affected (usually when there is more than one time point), annotate to the process in addition to the anatomy.
# Annotate to both general omim id, as well as the alleles.
#* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles. when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
#*Sometimes there is phenotype data in the body of the OMIM record (eg. general OMIM ID) that does not refer to an allelic variant. However, many times in the body of the OMIM record it does in fact use the allelic variant ID (and refers to the allelic variants section). In this case, we don't need to record it for the general ID AND the allelic variant, just the allelic variant. Think of the general OMIM ID (as we are using it) as being all non-indicated alleles, rather than a general phenotype description of all alleles.
# When a PATO term is missing, always annotate to the next most specific term. If a branch is missing, annotate to the general term "quality".
# use standard notation like OMIM:1234567.0001/OMIM:1234567.0001 to indicate known homozygosity
# use OMIM:1234567.0001/+ to indicate known heterozygosity
# use OMIM:1234567.0001/OMIM:1234567.0002 to indicate any known trans-het
# indicate dominance/recessiveness in the Genetic Context box.
# if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
# mark annotations as 'abnormal', except in the case of 'remarkable normality'. (see below)
# dates that annotations are created will be set automatically in the background by phenote.
# be sure to indicate incomplete_penetrance in the cases where multiple family members are described with the same genotype but different phenotypes.

==Remarkable Normality==
There is a special case wherein a particular phenotype character is expected, and is observed NOT to occur, or what we call 'remarkable normality'.
But this truly is a reflection of one 'normal' phenotype ''in comparison'' to the 'mutant' phenotype.
# in the first pass, be sure to list the phenotype as it is listed in the other mutants, but add the qualifier of 'normal'.
==Comparative Statements==

OMIM Annotation Standards

2007-11-05T22:45:58Z

Nicolew: /* Basic Rules */

This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax.

==Basic Rules==
# Use the ncbo 'config'. This will include automatic updates to the latest ontologies from SF.
# No use of MP, though it can be used to look for good cross-products
# Use the same style for gene ids. ie. OMIM:601653.0005 (database:identifier dot allele designation)
# no postcomposition using GO:Biological_Process with a continuant
# limit the post-comp relation to part_of. we can discuss this- but this is what we do at zfin, so at least the zebrafish data is biased in this way already
# If its known that a process is affected (usually when there is more than one time point), annotate to the process in addition to the anatomy.
# Annotate to both general omim id, as well as the alleles.
#* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles. when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
#*Sometimes there is phenotype data in the body of the OMIM record (eg. general OMIM ID) that does not refer to an allelic variant. However, many times in the body of the OMIM record it does in fact use the allelic variant ID (and refers to the allelic variants section). In this case, we don't need to record it for the general ID AND the allelic variant, just the allelic variant. Think of the general OMIM ID (as we are using it) as being all non-indicated alleles, rather than a general phenotype description of all alleles.
# When a PATO term is missing, always annotate to the next most specific term. If a branch is missing, annotate to the general term "quality".
# use standard notation like OMIM:1234567.0001/OMIM:1234567.0001 to indicate known homozygosity
# use OMIM:1234567.0001/+ to indicate known heterozygosity
# use OMIM:1234567.0001/OMIM:1234567.0002 to indicate any known trans-het
# indicate dominance/recessiveness in the Genetic Context box.
# if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
# mark annotations as 'abnormal', except in the case of 'remarkable normality'. (see below)
# dates that annotations are created will be set automatically.

==Remarkable Normality==
There is a special case wherein a particular phenotype character is expected, and is observed NOT to occur, or what we call 'remarkable normality'.
But this truly is a reflection of one 'normal' phenotype ''in comparison'' to the 'mutant' phenotype.
# in the first pass, be sure to list the phenotype as it is listed in the other mutants, but add the qualifier of 'normal'.
==Comparative Statements==

OMIM Annotation Standards

2007-11-05T20:50:37Z

Nicolew: New page: This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax. ==Basic Rules=...

This page is to describe the rules that the NCBO curators are employing for translating the OMIM gene/disease description pages into phenotype statements using EQ syntax.

==Basic Rules==
# Use the ncbo 'config'. This will include automatic updates to the latest ontologies from SF.
# No use of MP, though it can be used to look for good cross-products
# Use the same style for gene ids. ie. OMIM:601653.0005 (database:identifier dot allele designation)
# no postcomposition using GO:Biological_Process with a continuant
# limit the post-comp relation to part_of. we can discuss this- but this is what we do at zfin, so at least the zebrafish data is biased in this way already
# If its known that a process is affected (usually when there is more than one time point), annotate to the process in addition to the anatomy.
# Annotate to both general omim id, as well as the alleles.
#* Meaning, there is a general description of the phenotype for affected genes at the top of the OMIM page, so annotate that in addition to the phenotypes that are listed for the specific alleles. when annotating to the general description, use the omim identifier without an allele designation (ie OMIM:601653) only
# When a PATO term is missing, always annotate to the next most specific term. If a branch is missing, annotate to the general term "quality".
# use standard notation like OMIM:1234567.0001/OMIM:1234567.0001 to indicate known homozygosity
# use OMIM:1234567.0001/+ to indicate known heterozygosity
# use OMIM:1234567.0001/OMIM:1234567.0002 to indicate any known trans-het
# indicate dominance/recessiveness in the Genetic Context box.
# if OMIM:1234567.0001 is listed without the second allele indicated, this notation indicates unknown het/homo?
# mark annotations as 'abnormal', except in the case of 'remarkable normality'. (see below)

==Remarkable Normality==
There is a special case wherein a particular phenotype character is expected, and is observed NOT to occur, or what we call 'remarkable normality'.
But this truly is a reflection of one 'normal' phenotype ''in comparison'' to the 'mutant' phenotype.
# in the first pass, be sure to list the phenotype as it is listed in the other mutants, but add the qualifier of 'normal'.
==Comparative Statements==

Phenote:Main Page

2007-11-05T19:59:22Z

Nicolew: /* Sandbox */

Phenote:Main Page

2007-10-24T23:29:22Z

Nicolew: /* Phenote Working Group */

Phenote:Main Page

2007-10-24T23:21:50Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Agenda: October 2, 2007

2007-10-03T21:59:49Z

Nicolew: Phenote:Agenda: October 2, 2007 moved to Phenote:Minutes: October 2, 2007: WE had the meeting

#REDIRECT [[Phenote:Minutes: October 2, 2007]]

Phenote:Minutes: October 2, 2007

2007-10-03T21:59:49Z

Nicolew: Phenote:Agenda: October 2, 2007 moved to Phenote:Minutes: October 2, 2007: WE had the meeting

==Presentation==

*A presentation by Jim Balhoff of NESCent describing the newest features for Phenote for the PhenoMap project.
Meeting information:

Topic: Phenote User Meeting
Date: Tuesday, October 2, 2007
Time: 8:30 am, Pacific Daylight Time (GMT -07:00, San Francisco )
Meeting Number: 553 774 275
Meeting Password: phenote

You can get to the WebEx software with the following link:
-------------------------------------------------------
[https://geneontology.webex.com/geneontology/j.php?ED=92628972&UID=47342867| Join the online meeting]
-------------------------------------------------------
1. Go to https://geneontology.webex.com/geneontology/j.php?ED=92628972&UID=47342867
2. Enter your name and email address.
3. Enter the meeting password: phenote
4. Click "Join".

-------------------------------------------------------
For assistance
-------------------------------------------------------
1. Go to https://geneontology.webex.com/geneontology/mc
2. Click "Assistance".
3. Click "Support".

==New Phenote features==

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Q&A==

==Administrative items==
*Moving meeting to an alternate day/time (to avoid some conflicts)

==In attendance==

Phenote:Main Page

2007-10-01T22:28:40Z

Nicolew: /* Joining the Working Group IRC chat */

Phenote:Minutes: October 2, 2007

2007-10-01T22:26:07Z

Nicolew:

Phenote:Minutes: October 2, 2007

2007-10-01T22:25:34Z

Nicolew: /* Presentation */

Phenote:Minutes: October 2, 2007

2007-10-01T22:22:38Z

Nicolew: New page: ==Presentation== *A presentation by Jim Balhoff of NESCent describing the newest features for Phenote for the PhenoMap project. ==New Phenote features== ==What's *bug*ing you?== *UI ann...

==Presentation==

*A presentation by Jim Balhoff of NESCent describing the newest features for Phenote for the PhenoMap project.

==New Phenote features==

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Q&A==

==Administrative items==
*Moving meeting to an alternate day/time (to avoid some conflicts)

==In attendance==

Phenote:Main Page

2007-10-01T22:21:06Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Main Page

2007-09-12T23:21:27Z

Nicolew: /* Phenote Working Group */

Phenote:Main Page

2007-08-07T21:25:15Z

Nicolew: /* Phenote Working Group */

Phenote:Main Page

2007-08-07T21:25:03Z

Nicolew: /* Phenote Developers Group */

Phenote:Main Page

2007-08-07T21:24:11Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Agenda: August 7, 2007

2007-08-06T22:48:22Z

Nicolew: New page: There's no specific agenda items for today. However, please bring any questions you might have to the floor.

There's no specific agenda items for today. However, please bring any questions you might have to the floor.

Phenote:Main Page

2007-08-06T22:39:38Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Main Page

2007-08-06T22:39:08Z

Nicolew: /* Phenote Working Group */

Special:Badtitle/NS200:Main Page

2007-07-31T19:24:35Z

Nicolew: /* Annotation tools that utilize PATO */

==PATO - Phenotypic Quality Ontology==

This wiki page currently serves as the home page for the PATO project and related efforts

=== What is PATO? ===

PATO is an ontology of '''phenotypic qualities''', intended for use in a
number of applications, primarily defining composite phenotypes and phenotype annotation.

For more details, see

* [[PATO:About]]

==Resources==

the NCBO will be developing resources to support PATO.

===Annotation data involving PATO===

No centralised repository yet. See

* [[PATO:Annotations]]

===Annotation tools that utilize PATO===

* http://phenote.org

===Phenotype Ontologies===

These will soon be available from [[NCBO BioPortal]]. For now you should just obtain them from http://obo.sourceforge.net/browse.html

; [http://obo.sourceforge.net/cgi-bin/detail.cgi?quality PATO] : Phenotypic qualities that form the building blocks of phenotype descriptions. Also available [http://purl.org/obo/owl/PATO in OWL]
; [http://obo.sourceforge.net/cgi-bin/detail.cgi?mammalian_phenotype Mammalian Phenotype]: Composite phenotype terms for the description of phenotype in Mammalia
; [http://obo.sourceforge.net/cgi-bin/detail.cgi?plant_trait Plant Trait]: Composite phenotype terms for phenotype in plants
; Yeast
; Worm

See [[PATO:Pre_vs_Post_Coordinating]] for preliminary work on reconciling the pre vs post composition approaches

===Request tracker===

You can use the tracker (currently hosted on sourceforge) to request new terms or suggest modifications

* [http://sourceforge.net/tracker/?group_id=76834&atid=595654 PATO Request tracker on sourceforge]

Requests for new terms should preferably come attached with proposed definitions and sources for those definitions

===Mail list===

The OBO Phenotype list is for discussion of phenotypes in general (not restricted to PATO)

You can subscribe or browse the archives here:

* [https://lists.sourceforge.net/lists/listinfo/obo-phenotype OBO-Phenotype Mail List]

The mail list is for discussion of PATO and phenotype annotation in general

==Meetings and Events==

* [[PATO_Meeting]] - Phenotype ontology meeting in Palo Alto, CA, December 1-2

==Presentations, papers and external links==

* [[Media:pato-stanford-nov-2006.ppt]]

Phenote:Main Page

2007-07-03T23:50:05Z

Nicolew:

Phenote:Minutes: July 3, 2007

2007-07-03T23:46:03Z

Nicolew: /* Talking points */

==Talking points==
*Developers discussed their current items:
**Jim discussed features he's currently developing. He's adding a new configurable item called "groups". For his use-case, it will allow a user to select one or more specimens to attribute a phenotype character. Its a shortcut that will translate into several rows in a spreadsheet.
**Nicole is working on processing & displaying both intra and inter-ontology cross-products. (see the terminfo pic below)
**Mark has started working on a configuration GUI, which is partially done, but not complete. He is currently working on the ability for external applications to communicate with phenote via http requests.
*Midori reflected that the new docking framework in oboedit is nice and cool and thought it might add to phenote.
*Developers decided to have a separate bi-weekly phone conference, 2nd and 4th Tuesdays, 10:30am. However, for July, these will take place on the 17th and 31st.

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
(no discussion)

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*delete problem [[https://sourceforge.net/tracker/index.php?func=detail&aid=1731871&group_id=76834&atid=887913 1731871]]
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*command line mode for file format conversion [[https://sourceforge.net/tracker/index.php?func=detail&aid=1744598&group_id=76834&atid=887913 1744598]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*display xrefs (& links) in term info window [[https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913 1739399]]
#*checks for relational qualities [[https://sourceforge.net/tracker/index.php?func=detail&aid=1737568&group_id=76834&atid=887913 1737568]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==
(none)
==Administrative items==
(none)
==In attendance==
Mark Gibson, Nicole Washington, Jim Balhoff, Midori Harris, David Sutherland

Phenote:Minutes: July 3, 2007

2007-07-03T23:43:22Z

Nicolew: New page: ==Talking points== *Developers discussed their current items: **Jim discussed features he's currently developing. He's adding a new configurable item called "groups". For his use-case, i...

==Talking points==
*Developers discussed their current items:
**Jim discussed features he's currently developing. He's adding a new configurable item called "groups". For his use-case, it will allow a user to select one or more specimens to attribute a phenotype character. Its a shortcut that will translate into several rows in a spreadsheet.
**Nicole is working on processing & displaying both intra and inter-ontology cross-products. (see the terminfo pic below)
**Mark has started working on a configuration GUI, which is partially done, but not complete. He is currently working on the ability for external applications to communicate with phenote via http requests.
*Midori reflected that the new docking framework in oboedit is nice and cool and thought it might add to phenote.

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
(no discussion)

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*delete problem [[https://sourceforge.net/tracker/index.php?func=detail&aid=1731871&group_id=76834&atid=887913 1731871]]
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*command line mode for file format conversion [[https://sourceforge.net/tracker/index.php?func=detail&aid=1744598&group_id=76834&atid=887913 1744598]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*display xrefs (& links) in term info window [[https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913 1739399]]
#*checks for relational qualities [[https://sourceforge.net/tracker/index.php?func=detail&aid=1737568&group_id=76834&atid=887913 1737568]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==
(none)
==Administrative items==
(none)
==In attendance==
Mark Gibson, Nicole Washington, Jim Balhoff, Midori Harris, David Sutherland

Phenote:Main Page

2007-07-03T23:37:28Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Agenda: July 3, 2007

2007-07-02T23:47:37Z

Nicolew: /* Setting priorities */

==Talking points==

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*delete problem [[https://sourceforge.net/tracker/index.php?func=detail&aid=1731871&group_id=76834&atid=887913 1731871]]
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*command line mode for file format conversion [[https://sourceforge.net/tracker/index.php?func=detail&aid=1744598&group_id=76834&atid=887913 1744598]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*display xrefs (& links) in term info window [[https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913 1739399]]
#*checks for relational qualities [[https://sourceforge.net/tracker/index.php?func=detail&aid=1737568&group_id=76834&atid=887913 1737568]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==

==In attendance==

Phenote:Agenda: July 3, 2007

2007-07-02T23:47:20Z

Nicolew: /* Setting priorities */

==Talking points==

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*delete problem [[https://sourceforge.net/tracker/index.php?func=detail&aid=1731871&group_id=76834&atid=887913 1731871]]
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*command line mode for file format conversion [[https://sourceforge.net/tracker/index.php?func=detail&aid=1744598&group_id=76834&atid=887913 1744598]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*display xrefs (& links) in term info window [[https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913 1739399]]
#*checks for relational qualities [[https://sourceforge.net/tracker/index.php?func=detail&aid=1737568&group_id=76834&atid=887913 1737568]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]

#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==

==In attendance==

Phenote:Agenda: July 3, 2007

2007-07-02T23:45:40Z

Nicolew: /* Setting priorities */

==Talking points==

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*delete problem [[https://sourceforge.net/tracker/index.php?func=detail&aid=1731871&group_id=76834&atid=887913]]
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*command line mode for file format conversion
[[https://sourceforge.net/tracker/index.php?func=detail&aid=1744598&group_id=76834&atid=887913]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*display xrefs (& links) in term info window
[[https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913]]
#*checks for relational qualities [[https://sourceforge.net/tracker/index.php?func=detail&aid=1737568&group_id=76834&atid=887913]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]

#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==

==In attendance==

Phenote:Agenda: July 3, 2007

2007-07-02T23:40:00Z

Nicolew:

==Talking points==

==New Phenote features==
*Update: Cross-product display
**Whatcha think of this kind of cross-product display?
[[Image:So xp terminfo.png]]

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==

==In attendance==

File:So xp terminfo.png

2007-07-02T23:38:50Z

Nicolew:

Phenote:Agenda: July 3, 2007

2007-07-02T23:38:33Z

Nicolew: /* New Phenote features */

==Talking points==

==New Phenote features==
Whatcha think of this kind of cross-product display?
[so_xp_terminfo.png]

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==

==In attendance==

Phenote:Agenda: July 3, 2007

2007-07-02T23:26:32Z

Nicolew: New page: ==Talking points== ==New Phenote features== ==What's *bug*ing you?== *UI annoyances *New bugs? ==Setting priorities== #Top 10 Highest priorities from tracker: #*loading status & descri...

==Talking points==

==New Phenote features==

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==

==In attendance==

Phenote:Main Page

2007-07-02T23:08:43Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Main Page

2007-06-12T00:29:51Z

Nicolew: /* Phenote Working Group */

PhenoMaP060507

2007-06-06T00:48:05Z

Nicolew: New page: Rough minutes from Phenote workgin group meeting with Nescent 5th June 2007 Jim Balhoff: 1. How to apply EQ to evolutionary characters Coming to method closer to that being used for Mut...

Rough minutes from Phenote workgin group meeting with Nescent 5th June 2007

Jim Balhoff:

1. How to apply EQ to evolutionary characters

Coming to method closer to that being used for Mutant phenotypes than thought would at first.

-> phenote interface style OK

2. workflows

Starting with a a paper -> set of specimens. They will often want to make statements about subsets

Might want to make say one statement about catfish and one about salmon...

Hilmar

ONe thing that would be extreemly useful for us is to do some upfront setup work.. There are lots of things that will pertain to everything you will record for one paper.

You want to be able to record in advance what the species are

Paula - the examplar approach - we are envisioing setup starting with listing examplars.

So - you put in your speciment list first.

Since you'll be using a taxonomy - if you want to have a shortcut where you can apply a statement to all members of a group.

But some issue of how this is linked - best linked to exemplar species. It is a hypothesis that something applies to all because it applies to exemplars.

MA: Each order will I presume have a set of EQ pairs which differentiate - and all the way down through orders, families, species etc

Then all you would have to enter is the differentii for species specificity.

Paula says - this is putting conclusions first - need to keep data linked to observation.

Jim Balhoff

Bringing it back to practicalities:

What we need is a shortcut that allows you to choose a taxonomic grouping and then automatically generate the complete set of statements for examplars used in that paper for that grouping.

Hilmar

Two more things

1. PATO:

JIM - attribute and value slims - has anyone else found a use for these? Presumably these will need to be maintained. We still think they will be valuable to us.

Paula - I would think that the phenotypic data should require these slims.
DS: Think most likely to be useful for front end - analysis tools for PO annotated data.

2. Character Matrices:

Character matrix view of the data needs to be easily accessible. Press a button and convert phenote table view to character matrix (presumably using attributes slim).

Jim has written something for this - only works in one direcetion (phenote -> character matrix ) right now.

[MA - says something about spider phenotype ontology - Nicole working with these people...]

BIRN - interested in charcter matrices. - according to Nicole just interested in this as a particular view.

"If we are to adopt phenote as a basis for our editor, we would certainly be in a position to play a major driving role".

Mark asked - Is this interest in phenote web based:

A: Not sure.

What are your goals over the next few months:

Mark:

1. config GUI

2. Tab system - one tab informs another - this will work for genotypes.

A: That sounds really useful

Nicole: Could use this to set up all the exemplary species.

3. Output in obo annotation format - or at least in form that can merge with. But - would still keep XML based data adapters. (DS noted that XML output needed for FB).

Nicole - likely to be more discussion of this new format in a couple of weeks.

Mark

web vs stand-alone

Nescent likes web because distributed curators.

BIRN - will integrate phenote into their apps.

Melissa: I think stand-alone is better becuase much more configurable - so much better to start with this to iron out wrinkles; easy to share data files; easy to manipulate configuration.

Phenote:Minutes: June 5, 2007

2007-06-06T00:45:31Z

Nicolew: /* Talking points */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am.
**see summary of discussion ([[PhenoMaP060507]])
* numbering of configs & versioning
**decided that for NCBO, Nicole would be the 'gatekeeper' of the configuration. Any modifications to the configuration would be discussed/decided within the larger group, then Nicole will update the configuration on the server. The idea will be that major changes would happen on the server, then be distributed via the webstart application. This will probably be the method that zfin will also take as a means to distribute a version to their collaborating labs. We'll set it up so that the user's will always get the most updated version from the webstart.
**Note that this is a pretty good policy for groups to keep in mind. Although this is not the overall policy. Probably needs to be decided within each community.
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?
** punted to the obo-phenote mailing list
*solicitation for information about 'expression' configuration. this is a hot topic right now. many groups want to be annotating expression phenotypes. will start discussion on the obo-phenote mailing list, but will set up a obo-phenote-expression list.

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Minutes: June 5, 2007

2007-06-06T00:45:03Z

Nicolew: /* Talking points */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am.
**see summary of discussion [[PhenoMaP060507 here]]
* numbering of configs & versioning
**decided that for NCBO, Nicole would be the 'gatekeeper' of the configuration. Any modifications to the configuration would be discussed/decided within the larger group, then Nicole will update the configuration on the server. The idea will be that major changes would happen on the server, then be distributed via the webstart application. This will probably be the method that zfin will also take as a means to distribute a version to their collaborating labs. We'll set it up so that the user's will always get the most updated version from the webstart.
**Note that this is a pretty good policy for groups to keep in mind. Although this is not the overall policy. Probably needs to be decided within each community.
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?
** punted to the obo-phenote mailing list
*solicitation for information about 'expression' configuration. this is a hot topic right now. many groups want to be annotating expression phenotypes. will start discussion on the obo-phenote mailing list, but will set up a obo-phenote-expression list.

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Minutes: June 5, 2007

2007-06-06T00:39:18Z

Nicolew: /* Setting priorities */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am.
**see summary of discussion [[ here]]
* numbering of configs & versioning
**decided that for NCBO, Nicole would be the 'gatekeeper' of the configuration. Any modifications to the configuration would be discussed/decided within the larger group, then Nicole will update the configuration on the server. The idea will be that major changes would happen on the server, then be distributed via the webstart application. This will probably be the method that zfin will also take as a means to distribute a version to their collaborating labs. We'll set it up so that the user's will always get the most updated version from the webstart.
**Note that this is a pretty good policy for groups to keep in mind. Although this is not the overall policy. Probably needs to be decided within each community.
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?
** punted to the obo-phenote mailing list
*solicitation for information about 'expression' configuration. this is a hot topic right now. many groups want to be annotating expression phenotypes. will start discussion on the obo-phenote mailing list, but will set up a obo-phenote-expression list.

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?
#*want to move the priority of "live reconfigure" higher than the GUI. since it is a necessary part of the GUI configuration spec anyway, will work on this first.
#*want to move up saving changes to 'term history' display preferences

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Minutes: June 5, 2007

2007-06-06T00:37:29Z

Nicolew: /* Talking points */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am.
**see summary of discussion [[ here]]
* numbering of configs & versioning
**decided that for NCBO, Nicole would be the 'gatekeeper' of the configuration. Any modifications to the configuration would be discussed/decided within the larger group, then Nicole will update the configuration on the server. The idea will be that major changes would happen on the server, then be distributed via the webstart application. This will probably be the method that zfin will also take as a means to distribute a version to their collaborating labs. We'll set it up so that the user's will always get the most updated version from the webstart.
**Note that this is a pretty good policy for groups to keep in mind. Although this is not the overall policy. Probably needs to be decided within each community.
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?
** punted to the obo-phenote mailing list
*solicitation for information about 'expression' configuration. this is a hot topic right now. many groups want to be annotating expression phenotypes. will start discussion on the obo-phenote mailing list, but will set up a obo-phenote-expression list.

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Minutes: June 5, 2007

2007-06-06T00:22:52Z

Nicolew: /* In attendance */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am
* numbering of configs & versioning
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Schindelman, Yvonne Bradford, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Minutes: June 5, 2007

2007-06-06T00:21:22Z

Nicolew: /* Administrative items */

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am
* numbering of configs & versioning
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Sharpen, Yvonne, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Main Page

2007-06-06T00:14:31Z

Nicolew: /* Members */

Phenote:Minutes: June 5, 2007

2007-06-05T19:39:23Z

Nicolew: New page: ==Talking points== * joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am * numbering of configs & versioni...

==Talking points==
* joint meeting with NESCent to discuss user interfaces and workflows for their [http://phenomap.nescent.org PhenoMaP] project 8:30-9am
* numbering of configs & versioning
* display of post composed terms in the table. how do you like the current display? if you don't like it, what might be 'prettier' or better for understanding?

==New Phenote features==
05.24.2007, version 1.3 released
* feature: Web-based documentation and Help features [http://www.phenote.org/help check it out here]
* feature: Metadata fields added to configuration. User can name their configuration, add a description, and author
* feature: Descriptions can be added for fields
* feature: Master-to-local overwrite stuff
* feature: Dialog allows user to back out of exiting from File->Exit
* feature: Autocompletion search default settings configurable
* feature: User can save search setting defaults if changed during Phenote session
* feature: Added sample config for BIRN
* feature: Added SAO.obo ontology for BIRN
* feature: Namespace config writes back
* feature: Can specify more than one website for ontology update
* feature: Empty field shows all terms in ontology rather than none
* feature: Can add more differentia to post comp
* change: File->New is disabled until next version
* change: ncbo, zfin-standalone, flybase, demo configurations modified to include master-overwrite feature; keeping track of revision history in file comments
* change: can read http, https, ftp, ftps for ontology update URLs, not just http [1718945]
* bugfix: Bulk-editing functions are working again
* bugfix: Undo wasn't working for several functions due to a bug in the Copy function [ 1721044]
* bugfix: multi-select deletes free-text content replaces with * [1721032]
* bugfix: pre 1.2 post comp data wasnt able to load [1721470]
* bugfix: Config update/merge bug where fields in wrong order fixed.

==What's *bug*ing you?==
*UI annoyances
*New bugs?

==Setting priorities==
#Top 10 Highest priorities from tracker:
#*loading status & description [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669587&group_id=76834&atid=887913 1669587]]
#*gui for configuration [[https://sourceforge.net/tracker/index.php?func=detail&aid=1671204&group_id=76834&atid=887913 1671204]]
#*no autocomplete on a few characters/configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1592012&group_id=76834&atid=887913 1592012]]
#*tracking annotation date & assign_by [[https://sourceforge.net/tracker/index.php?func=detail&aid=1727981&group_id=76834&atid=887913 1727981]]
#*tabbed field panel, configurable [[https://sourceforge.net/tracker/index.php?func=detail&aid=1677389&group_id=76834&atid=887913 1677389]]
#*"enter" does not accept text fields [[https://sourceforge.net/tracker/index.php?func=detail&aid=1600656&group_id=76834&atid=887913 1600656]]
#*click on table cell to move cursor to that field [[https://sourceforge.net/tracker/index.php?func=detail&aid=1594468&group_id=76834&atid=887913 1594468]]
#*clear all/start over [[https://sourceforge.net/tracker/index.php?func=detail&aid=1579368&group_id=76834&atid=887913 1579368]]
#*user specified default settings [[https://sourceforge.net/tracker/index.php?func=detail&aid=1669561&group_id=76834&atid=887913 1669561]]
#*right-click functionality [[https://sourceforge.net/tracker/index.php?func=detail&aid=1670429&group_id=76834&atid=887913 1670429]]
#Are these still important?
#Are there other items of higher priority?

==Q&A==

==Administrative items==
*Time/date ok?
*New: Separating out features from bug requests:
**Please use the "Group" category of "new feature" when submitting a new feature request.

==In attendance==
Mark Gibson, Nicole Washington, Melissa Handell, David Sutherland, Gary Sharpen, Yvonne, Midori Harris, Michael Ashburner, Hilmar Lapp, Jim Balhoff, Paula Mabee

Phenote:Main Page

2007-06-05T18:59:17Z

Nicolew: /* Phenote:Agendas & Transcripts */

Phenote:Main Page

2007-06-05T15:24:25Z

Nicolew: /* Phenote Working Group */