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.

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 not yet scheduled the next teleconference.

Phenote Working Group

The Phenote User group will meet via WebEx on Wednesday, September 10th, 2008, at 9:00am PDT.

The goals of the Phenote Users Group are to:

1. drive the development of the software by prioritizing features
2. test new beta releases; report and prioritize bug fixes
3. sign off on new releases for the general public
4. update and add to to documentation

Joining the Working Group WebEx Chat

Webex Instructions:

Topic: Phenote monthly meeting Date: Wednesday, September 10, 2008 Time: 9:00 am, Pacific Daylight Time (GMT -07:00, San Francisco) Meeting Number: 555 311 453 Meeting Password: phenote

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To join the online meeting

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1. Go to https://geneontology.webex.com/geneontology/j.php?ED=99523852&UID=0&PW=1b57613e3e5d58160a524557 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
• 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 [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:

PE: Dendrite length in microns, Phenote: user enters integer or float

PE: Brain-cell color, Phenote: user enters from drop down list of colors from pato

PE: Dendrite shape warped, Phenote: user checks true/false checkbox

To generalize there are 3 different types of Observables, all require an Entity:

1. A measurement of an Entity (including units), value to be recorded by entering it in Phenote
2. An attribute of an Entity, value to be recorded by selecting from a pick list in Phenote
3. The presence of a certain quality/value, to be recorded in Phenote by a checkbox (true/false)

For #2, 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 the matrix view the column headings would be each of the Observables defined beforehand in the PE. 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 phenotypic assertion (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?