GEORGETOWN UNIVERSITY (THE)
This is a CAREER award to support the research of Dr. Hongfang Liu in the Department of Biostatistics, Bioinformatics and Biomathematics at Georgetown University. Dr. Liu is a second-year, tenure-track Assistant Professor. Natural language processing (NLP) is a field of computer science and linguistics which develops algorithmns to locate concepts in free text; ontologies (ie. common, defined volcabulary) must be created to capture the meaning of the free text. The research field of this investigator is in the use of NLP for biological knowledge management. Specifically she will build NLP systems for protein form curation. NLP systems will be used for retrieving articles, highlighting sentences, and extracting events/relationships related to protein forms and used as a basis for curating proteins. Since one gene can produce multiple protein forms which differ in sequence, chemistry, and function, a systematic analysis of proteomics data is needed for accurate annotations of genes and their corresponding protein forms. A NLP system can be constructed by taking advantage of knowledge from existing NLP systems and the targeted end users of the system. The project is engaging various communities such as molecular database developers, NLP researchers, and basic biology scientists, as the expert knowledge base for tools development. All of the NLP tools for protein curation will be posted on the Liu lab website: http://explore.georgetown.edu/people/hl224/?action=viewgeneral&PageTemplateID=225
As a part of her CAREER plan, Dr. Liu is providing research-oriented educational experiences for students and young researchers, especially in NLP and in ontology-based knowledge management in biology. Several web-based mini courses are being developed to provide biological domain-specific introduction to ontology, NLP, and ontology-based tools. The courses will be distributed publically. The research team includes a post-doctoral associate and doctoral student and interns from related degree programs at Georgetown and from nearby universities, including several historically minority schools such as Howard University and University of the District of Columbia. These collaborations will increase the participation of women and minorities and others under-represented in science and technology.
Choose a quarter and click "Go."
| AWARD OVERVIEW |
| Award Number |
0845523 |
Funding Agency |
National Science Foundation |
| Total Award Amount |
$843,662 |
Project Location - City |
Washington |
| Award Date |
08/10/2009 |
Project Location - State |
DC |
| Project Status |
Less Than 50% Completed |
Project Location - Zip |
20057-1789
|
| Jobs Reported |
0.05 |
Congressional District |
01 |
| Project Location - Country |
US |
|
|
Recipient Information
(Grants)
| Recipient Information (Grants) |
|
Recipient Name
|
GEORGETOWN UNIVERSITY (THE) |
| Recipient DUNS Number |
049515844
|
| Recipient Address |
37TH & O STS NW |
| Recipient City |
WASHINGTON |
| Recipient State |
District of Columbia |
| Recipient Zip |
20057-0001 |
| Recipient Congressional District |
01 |
| Recipient Country |
USA |
Required to Report Top 5
Highly Compensated Officials |
No |
Projects and Jobs Information
| Projects and Jobs Information |
| Project Title |
Natural Language Processing for Biological Knowledge Management |
| Project Status |
Less Than 50% Completed |
| Final Project Report Submitted |
No |
| Project Activities Description |
Research Institutes & Public Policy Analysis |
| Quarterly Activities/Project Description |
1)The design and development of MutD, a literature mining system that associates point mutations with proteins as well as the resultant impact in phenotyping
2)Conduct evaluation of MutD based on a gold standard automatically assembled from UniProtKB
3)Submit a manuscript related to MutD to ISMB 2013
4)Investigate the lucene index mechanisms to index NLP annotations and corresponding free text so that query-based retrieval can be done on both free text and NLP annotations
5)Investigate the use of Semantic MEDLINE, RDF, and SPARQL for knowledge discovery
6)Attend several meetings: American Medical Informatics Association (AMIA) Annual Symposium 2012, Clinical and Translation Science Awards (CTSA) Annual Informatics Meeting 2012, Individualized Medicine Conference (IM) 2012
7)Set up plans to attend BioCreative 2013
Due to the PI relocation, the project was interrupted by one year and we plan to accelerate the progress in the coming two years! |
| Jobs Created |
0.05 |
| Description of Jobs Created |
Professor |
Purchaser Information
(Grants)
| Purchaser Information |
| Contracting Office ID |
Not Reported |
| Contracting Office Name |
Not Available |
| Contracting Office Region |
Not Available |
| TAS Major Program |
49-0101 |
| Award Information |
| Award Date |
08/10/2009 |
| Award Number |
0845523 |
| Order Number |
|
| Award Type |
Grants |
| Funding Agency ID |
49 |
| Funding Agency Name |
National Science Foundation |
| Funding Office Name |
Not Available |
| Awarding Agency ID |
49 |
| Awarding Agency Name |
National Science Foundation |
| Amount of Award |
$843,662 |
| Funds Invoiced/Received |
$120,538 |
| Expenditure Amount |
$120,538 |
| Infrastructure Expenditure Amount |
$0 |
| Infrastructure Purpose and Rationale |
Not Reported |
| Infrastructure Point of Contact Name |
Not Reported |
| Infrastructure Point of Contact Email |
Not Reported |
| Infrastructure Point of Contact Phone |
Not Reported |
| Infrastructure Point of Contact Address |
Not Reported |
| Infrastructure Point of Contact City |
Not Reported |
| Infrastructure Point of Contact State |
Not Reported |
| Infrastructure Point of Contact Zip |
Not Reported |
Product or Service Information
(Grants)
| Product or Service Information |
| Primary Activity Code |
U05 - NTEE |
| Activity Description |
Research Institutes & Public Policy Analysis |
| Sub-Awards Information |
| Sub-awards to Organizations |
0 |
| Sub-award Amounts to Organizations |
$0 |
| Sub-Awards to Individuals |
0 |
| Sub-Award Amounts to Individuals |
$0 |
| Number of Sub-awards less than $25,000/award |
0 |
| Amount of Sub-awards less than $25,000/award |
$0 |
| Number of payments to vendors greater than $25,000 |
0 |
| Total Amount of payments to vendors greater than $25,000/award |
$0 |
| Number of payments to vendors less than $25,000/award |
1 |
| Total Amount of payments to vendors less than $25,000/award |
$7,096 |
| Location Information |
| Latitude, Longitude |
38º 54' 27",
-77º 4' 17" |
| Congressional District |
01 |
| Address 1 |
37th & O Street NW |
| Address 2 |
|
| City |
Washington |
| County |
District of Columbia |
| State |
DC |
| Zip |
20057-1789 |
|
 |