Phenote:Main Page

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 Core 2 group with the National Center for Biomedical Ontology.

For more information, please visit the website at 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

• 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:

• 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:

1. drive the development of the software by prioritizing features
2. test new beta releases; reporting, and prioritizing bug fixes
3. sign off on new releases for the general public
4. 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
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To join the online meeting
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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 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. 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 [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; [Transcripts]

• Phenote:Agenda: August 7, 2007; [Transcripts]

• Phenote:Minutes: July 3, 2007; [Transcripts]

• Phenote:Minutes: June 5, 2007; [Transcripts]

• Phenote:Minutes: May 1, 2007; [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?