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Semantic Annotation of SF knowledge bases
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For the
effective management of SF knowledge, we are currently in the process
of organizing LFs according to their semantic categories. We adopted
eight semantic groups below, derived from the
UMLS semantic groups
[McCray et al. 2001]. For assignment of
semantic groups, we exploited existing knowledge sources in the domain
for the training of supervised machine learning model (see [Liu et al.
2001]). Currently, as a semantic group assignment system,
we use a maximum
entropy model [MaxEnt] trained over (a part of) the entries in the
ADAM database [Zhou et al. 2006] that we
automatically annotated with semantic groups according to the
UMLS [Bodenreider, 2006].
While the model considers with contextual features as well as phrase
internal features (see [Torii et al. 2005]), only the phrase internal
clues are used for this web demo.
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Groups
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UMLS
Semantic Types
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ANAT
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Anatomical
Structure, Body Location or Region, Body Part, Organ, or Organ
Component, Body Space or Junction, Body Substance, Body System, Cell,
Cell Component, Embryonic Structure, Fully Formed Anatomical Structure,
Tissue
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CHEM
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Amino
Acid Sequence, Amino Acid, Peptide, or Protein, Antibiotic,
Biologically Active Substance, Biomedical or Dental Material,
Carbohydrate, Carbohydrate Sequence, Chemical, Chemical Viewed
Functionally, Chemical Viewed Structurally, Clinical Drug, Eicosanoid,
Element, Ion, or Isotope, Enzyme, Gene or Genome, Hazardous or
Poisonous Substance, Hormone, Immunologic Factor, Indicator, Reagent,
or Diagnostic Aid, Inorganic Chemical, Lipid, Molecular Sequence,
Neuroreactive Substance or Biogenic Amine, Nucleic Acid, Nucleoside, or
Nucleotide, Nucleotide Sequence, Organic Chemical, Organophosphorus
Compound, Pharmacologic Substance, Receptor, Steroid, Vitamin
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CONC
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Classification,
Conceptual Entity, Functional Concept, Group Attribute, Idea or
Concept, Intellectual Product, Language, Qualitative Concept,
Quantitative Concept, Regulation or Law, Spatial Concept, Temporal
Concept
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DISO
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Acquired
Abnormality, Anatomical Abnormality, Cell or Molecular Dysfunction,
Congenital Abnormality, Disease or Syndrome, Experimental Model of
Disease, Finding, Injury or Poisoning, Mental or Behavioral
Dysfunction, Neoplastic Process, Pathologic Function, Sign or Symptom
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LIVB
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Age
Group, Alga, Amphibian, Animal, Archaeon, Bacterium, Bird, Family
Group, Fish, Fungus, Group, Human, Invertebrate, Mammal, Organism,
Patient or Disabled Group, Plant, Population Group, Professional or
Occupational Group, Reptile, Rickettsia or Chlamydia, Vertebrate, Virus
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PHYS
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Cell
Function, Clinical Attribute, Genetic Function, Mental Process,
Molecular Function, Organ or Tissue Function, Organism Attribute,
Organism Function, Physiologic Function
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PROC
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Diagnostic
Procedure, Educational Activity, Health Care Activity, Laboratory
Procedure, Molecular Biology Research Technique, Research Activity,
Therapeutic or Preventive Procedure
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OTHERS
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Activity,
Behavior, Biologic Function, Biomedical Occupation or Discipline, Daily
or Recreational Activity, Drug Delivery Device, Entity, Environmental
Effect of Humans, Event, Food, Geographic Area, Governmental or
Regulatory Activity, Health Care Related Organization, Human-caused
Phenomenon or Process, Individual Behavior, Laboratory or Test Result,
Machine Activity, Manufactured Object, Medical Device, Natural
Phenomenon or Process, Occupation or Discipline, Occupational Activity,
Organization, Phenomenon or Process, Physical Object, Professional
Society, Research Device, Self-help or Relief Organization, Social
Behavior, Substance
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Bodenreider O. (2004) The Unified
Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 32(Database issue):D267-270.
Liu H, Lussier Y and Friedman C (2001) Disambiguating Biomedical Terms in Biomedical Narrative Text: an Unsupervised Journal of Biomedical Informatics, Elsevier Ltd., 34 (4): 249-61.
MaxEnt.http://maxent.sourceforge.net/.
McCray
AT, Burgun A, Bodenreider O (2001) Aggregating UMLS semantic
types for
reducing conceptual complexity. Proceedings of Medinfo;10(Pt
1):216-20.
Torii M, Kamboj S and Vijay-Shanker K (2005) Using name-internal and contextual features to classify biological terms. Journal of Biomedical Informatics, 37, pp.498–511.
Torii
M and Liu H (2006) Headwords and Suffixes in Biomedical
Names. In proc of Knowledge Discovery in Life Science
Literature (KDLL), pp.29-41.
Zhou W, Torvik VI, Smalheiser NR (2006) ADAM: another database of
abbreviations in MEDLINE. Bioinformatics;
22(22): 2813-2818.
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Liu
Lab, Building D, Room 175, 4000 Reservoir Rd NW, Washington, DC
20007 | Phone: 202.687.7933 |Last updated:
February 26, 2007
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