NaCTeM

Annotation Tools

If you have some software which you would like us to add to this list, or if you would like us to change or remove an entry, please contact us.

ABNER
a downloadable Java API. ABNER is an information extraction tool capable of identifying gene and protein name from text and sgml input.
BioRAT
a downloadable Java API based PubMed article search and relationship extraction tool based on the GATE architecture (required).
Callisto
A java-based annotation tool support linguistic annotation of textual sources for any Unicode-supported language
FACTS
a downloadable Perl based functional annotation tool based on sequence similarity and text inferred data.
G2D
an information resource for disease associated RefSeq genes.
GAPSCORE
a webservice/web based gene and protein name finder.
GoMiner
a downloadable Java based search tool for identifying and clustering genes based on GO annotation hierarchies.
Harvester
a protein cross bioinformatic-database querying tool.
iProLINK
a searchable protein information resource, built on data extracted from PubMed, UniProt, Protein Information Resource (PIR) and GO.
KAT
a tool that expands the annotation information and MeSH description for queried SwissProt identifier(s) or those contained within the text of provided PubMed PMIDs.
KeX
a rule based gene and protein name finder which works from plain text or MEDLINE report formats.
Knowtator
A general-purpose text annotation tool that is integrated with the Protégé knowledge representation system. Knowtator facilitates the manual creation of training and evaluation corpora for a variety of biomedical language processing tasks.
LingPipe
a Java built linguisting annotator with built in MEDLINE tools for gene and protein identification.
MedBlast
a search tool for augmenting the sequence annotation information gathered from BLAST search results.
microGENIE
a sequence id annotation tool based on combining data from PubMed, UniGene and Swissprot.
MMax2
An annotation tool supporting arbitrarily many levels of annotation.
Semantic Gene Organizer
a search tool for clustering genes based on MEDLINE references.
Simple Rule Language (SRL) editor
SRL (Simple rule language) is a regular expression based language developed to perform fact extraction from plain text. The SRL Editor aims to supply built in support for hand-crafted rule testing and revision, e.g. to find text segments where no rules are matching or to find rules which do not match any text.
WordFreak
A java-based linguistic annotation tool designed to support human, and automatic annotation of linguistic data as well as employ active-learning for human correction of automatically annotated data.
XConc
A collection of XML-based tools which are integrated to support the corpus development and annotation.
XplorMed
a MEDLINE or uploaded article biomedical concept and concept relationship identification tool.