LINGUIST List 16.1509
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Thu May 12 2005
Calls: Computational Ling/USA; Anthro Ling/Socioling/USA
Editor for this issue: Amy Wronkowicz
<amy linguistlist.org>
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Directory
1. Kevin Bretonnel
Cohen,
Pacific Symposium on Biocomputing Session: Linking Biomedical Information through Text Mining
2. Erez
Levon,
New Ways of Analyzing Variation 34
Message 1: Pacific Symposium on Biocomputing Session: Linking Biomedical Information through Text Mining
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Date: 10-May-2005
From: Kevin Bretonnel Cohen <kevin.cohengmail.com>
Subject: Pacific Symposium on Biocomputing Session: Linking Biomedical Information through Text Mining
Full Title: Pacific Symposium on Biocomputing Session: Linking Biomedical
Information through Text Mining
Short Title: PSB
Date: 03-Jan-2006 - 07-Jan-2006
Location: Wailea, Maui, Hawai'i, United States of America
Contact Person: Kevin Bretonnel Cohen
Meeting Email: kevin.cohengmail.com
Web Site: http://psb.stanford.edu/cfp-nlp.html
Linguistic Field(s): Computational Linguistics
Call Deadline: 18-Jul-2005
Meeting Description:
The Pacific Symposium on Biocomputing, now in its eleventh year, is one of the
premier meetings in bioinformatics and computational biology. Its sessions on
'bioNLP' and on bio-ontologies over the past few years were the venue for
presentation of some of the highest-impact conference papers in these fields.
Motivation for this session
The past few years have seen a number of conference sessions and journal papers
on the topic of biomedical language processing, including PSB sessions in 2000,
2001, 2002, and 2003. Most of the systems discussed in this body of work have
identified entities or relations that are not grounded in any explicit external
model of the world, but rather simply point to substrings in the input text.
Such outputs are of intrinsically limited value. For example, a system that
produces a table of protein-protein interactions is potentially highly valuable
if it refers to specific entities in PDB, but of much more limited utility if it
outputs only a list of potentially ambiguous symbols and names.
Concomitant with the past several years' worth of work on mostly ungrounded
language processing systems, the past few years have seen a considerable body of
work on the linguistic and semantic characteristics of a variety of publicly
available biomedical data sources, including gene names and Gene Ontology terms.
Much of this work was presented at the PSB sessions on biomedical language
processing listed above or at PSB sessions on ontologies in 2003, 2004, and
2005. However, to date there has been only limited work on bringing these two
lines of pursuit together. The logical next step is to follow through on the
insights that we have gained into the structure of available data sources and
build language processing systems that can not only locate information in texts,
but map it to these explicit knowledge models. Two recent competitive evaluation
tasks from BioCreAtIvE (Critical Assessment of Information Extraction in
Biology) showed that it is possible both to build and to perform principled
evaluations of systems that produce grounded outputs. BioCreAtIvE Task 1(b)
involved mapping references to genes in free text to specific LocusLink entries.
BioCreAtIvE Task 2 involved assigning Gene Ontology terms to journal articles.
Taken together, these two tasks demonstrate that it is possible to link the
literature to specific entities and to specific concepts. At the same time, they
make it clear that there is considerable room for improvement in performance of
these tasks. This PSB session is intended to stimulate work in this area and to
drive progress both in language processing and in the use and development of
biological resources. It differs from previous PSB sessions on NLP and on
ontologies in that it requires that submissions include both an NLP component
and a mapping between at least two publicly available data sources.
Submission requirements
To encourage work that results in language processing systems whose output is
grounded with respect to public databases, submissions to this session will be
required to discuss work on some language processing system whose output
includes links between specific entries in at least two publicly available
biological data sources. We mean the term ''biological'' to exclude text
collections--for example, MEDLINE/PubMed can be the source of linking
assertions, but does not count as a biological data source. The prototypical
submission would be one describing work that uses MEDLINE/PubMed literature to
cross-connect two biological data sources, such as a system that assigns Gene
Ontology terms to LocusLink entries based on processing of MEDLINE/PubMed
abstracts, or one that links LocusLink entries to OMIM entries in the same way.
We will also accept submissions that are data-source-centric and do not involve
mining MEDLINE/PubMed as an intermediary data source, such as a paper on
locating Gene Ontology terms in OMIM gene function fields to link GO and OMIM.
However, all submissions must have a clear language processing component and
must establish clear connections between two or more publicly available
biological data sources.
We will define ''publicly available'' broadly. At least all NCBI-sponsored data
sources will qualify, as well as the biomedical vocabularies integrated in the
Unified Medical Language System (UMLS) Metathesaurus. We anticipate some, but
not all, potential sources to be:
- LocusLink/EntrezGene
- Gene Ontology
- MeSH
- OMIM
- HUGO
- DIP
- BIND
Session chairs
Kevin Bretonnel Cohen (Contact person)
Center for Computational Pharmacology
kevin.cohengmail.com
Olivier Bodenreider
National Library of Medicine
Lynette Hirschman
MITRE
Submission information
Papers and posters
The core of PSB consists of rigorously peer-reviewed full-length papers
reporting on original work. Accepted papers will be published in a cloth-bound
archival proceedings volume, indexed by MEDLINE/PubMed. The best of these will
be presented orally in plenary session.
Researchers wishing to present their research without official publication are
encouraged to submit a one-page abstract for the poster session.
Important dates
Paper submissions due: July 18, 2005
Notification of paper acceptance: September 6, 2005
Final versions due: September 23, 2005
Poster abstracts due: November 1, 2005
Meeting dates: January 3-7, 2006
Paper format
All papers must be submitted to Russ Altman in PostScript (.ps), Adobe Acrobat
(.pdf), or Microsoft Word (.doc) format. Adobe Acrobat is preferred. Attached
files should be named with the last name of the first author (e.g. altman.ps,
altman.pdf, or altman.doc). Hardcopy submissions or unprocessed TEX or LATEX
files will be rejected without review.
Every paper must be accompanied by a cover letter which must include the following:
The email address of the corresponding author
The specific PSB session that the paper or poster should be considered for
A statement that the submitted paper contains original, unpublished results, and
is not currently under consideration elsewhere
A statement that all authors concur with the contents of the paper
Submitted papers are limited to twelve (12) pages in the PSB publication format.
Please format your paper according to the instructions found at
http://psb.stanford.edu/psb-online/psb-submit/. If figures cannot easily be
resized and placed precisely in the text, then it should be clear that with
appropriate modifications, the total manuscript length would be within the page
limit.
Color pictures can be printed at the expense of the authors. The fee is $500 per
page of color pictures, payable at the time of camera-ready submission.
Contact Russ Altman (russ.altmanstanford.edu) for additional information about
paper submission requirements.
Message 2: New Ways of Analyzing Variation 34
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Date: 10-May-2005
From: Erez Levon <erez.levonnyu.edu>
Subject: New Ways of Analyzing Variation 34
Full Title: New Ways of Analyzing Variation 34
Short Title: NWAV 34
Date: 20-Oct-2005 - 23-Oct-2005
Location: New York, NY, United States of America
Contact Person: Renee Blake
Meeting Email: nwav34nyu.edu
Web Site: http://www.nwav34.com
Linguistic Field(s): Anthropological Linguistics; Sociolinguistics
Call Deadline: 01-Jun-2005
Meeting Description:
SECOND CALL FOR PAPERS
NWAV 34: Lects and the City will be held at New York University from October
20-23 2005. This year's theme highlights the linguistic and social issues that
arise in multicultural urban centers. Both a Thursday night plenary address and
a special Saturday night panel session will bring together scholars from
linguistics, anthropology, sociology and education to discuss ways of
approaching, conceiving of and researching urban areas, as well as the broader
implications of urban research.
Papers and posters: In addition to the panels and workshops with this focus, we
invite submissions for 20-minute papers in all areas of sociolinguistics.
Following the lead of previous NWAVs, we also encourage submissions for posters.
500-word abstracts are due on Wednesday June 1 2005. Abstracts may be submitted
electronically at our website (the preferred method), or via email to
nwav34nyu.edu. Online abstract submission forms are available on our website
(http://www.nwav34.com). Authors may submit an abstract for one singly-authored
paper/poster and one jointly-authored paper/poster, or two jointly-authored
papers/posters. Abstracts containing specialized fonts, characters or graphics
must be submitted in .pdf format. Abstracts for papers and posters will be
anonymously reviewed.
Panels: We will also be accepting proposals for a limited number of panel
sessions. Panel organizers must submit 500-word abstracts of the panel, which
include the participants' names, affiliations and contact information, via the
online submission form. In addition, panel organizers should submit individual
500-word abstracts for each of the panel participants. Panel sessions will be
100 minutes in length, and panel organizers may divide that time between
speakers/discussants as they wish. Participants on panels may also submit an
additional abstract for individual presentation, but must agree to withdraw
their singly-authored paper/poster if their panel is accepted. Abstracts for
panels will not be reviewed anonymously.
Notification of acceptance of papers, posters and panels will be emailed by July
1 2005.
Please note that sign language interpreting will be available for conference
participants, as needed. Those requiring interpreting must pre-register for the
conference, as well as indicate what sessions/talks they plan to attend, in
order to make appropriate arrangements. For further information on this or any
other aspects of the conference, please see updates on our website at
http://www.nwav34.com or contact:
Renée Blake
nwav34nyu.edu
NYU Linguistics
719 Broadway, 4th Floor
New York NY 10003
United States
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