MetaMap Installation - Revision history

Tejaswit: /* Versions (prototypes & releases) */

2010-01-28T04:42:28Z

Versions (prototypes & releases)

Tejaswit: /* Versions (prototypes & releases) */

2010-01-28T04:39:25Z

Versions (prototypes & releases)

Tejaswit: /* Collaboration & Acknowledgment */

2010-01-27T10:27:28Z

Collaboration & Acknowledgment

Tejaswit: /* Collaboration & Acknowledgment */

2010-01-27T10:26:37Z

Collaboration & Acknowledgment

Tejaswit: /* References */

2010-01-27T10:25:01Z

References

Tejaswit: /* References */

2010-01-27T10:24:41Z

References

Tejaswit: /* References */

2010-01-27T10:23:53Z

References

Tejaswit: /* References */

2010-01-27T10:23:39Z

References

Tejaswit: /* Presentation */

2010-01-27T10:16:59Z

Presentation

Tejaswit: /* Presentation */

2010-01-27T10:15:53Z

Presentation

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 == Versions (prototypes & releases) ==
-* December 2009 - Second Annotator prototype including MetaMap: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]
+* '''December 2009 - Second Annotator prototype including MetaMap: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]'''
 The release consists of an integrated MetaMap 2009 installation. The Data File builder utility was used build a custom dictionary containing the ontologies '''CST, OMS, 39857, 39046, 40187 and 39885'''. The data was obtained from the '''obs_v1_sept09''' schema. However, some ontologies like 39857 is not present in '''obs_v1_sept09'''
-* November 2009 - Second Annotator prototype including Mmtx: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]
+* '''November 2009 - Second Annotator prototype including Mmtx: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]'''
 The release consists of an integrated MMTx installation. The Data File builder utility was used build a custom dictionary containing all the ontologies in the '''obs''' schema. A defect with this installation is that the Data File builder scripts processed only CUIs of 8 digits length. This is a bug in the MMTx documentation.

@@ Line 23: / Line 23: @@
 * December 2009 - Second Annotator prototype including MetaMap: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]
-[Tejaswi: give detail about the release, and the problems of the installation e.g., the list of ontologies used]
 * November 2009 - Second Annotator prototype including Mmtx: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html]
-[Tejaswi: give detail about the release, and the problems of the installation e.g., the list of ontologies used]
 == References ==

@@ Line 32: / Line 32: @@
 == Collaboration & Acknowledgment ==
-We thank the guys at NLM [http://www.nlm.nih.gov/] for their constant support and help at various stages of this project.
+We thank the researchers at National Library of Medicine [http://www.nlm.nih.gov/] for their constant support and help at various stages of this project.
 == MetaMap Installation documentation ==

@@ Line 32: / Line 32: @@
 == Collaboration & Acknowledgment ==
-[a sentence to acknowledge the support of NLM]
+We thank the guys at NLM [http://www.nlm.nih.gov/] for their constant support and help at various stages of this project.
 == MetaMap Installation documentation ==

@@ Line 28: / Line 28: @@
 == References ==
-gforge code location
+* gforge code location https://bmir-gforge.stanford.edu/gf/project/obs/
 == Collaboration & Acknowledgment ==

← Older revision		Revision as of 10:24, 27 January 2010
Line 28:		Line 28:

	== References ==		== References ==
		+	gforge code location

	* https://bmir-gforge.stanford.edu/gf/project/obs/		* https://bmir-gforge.stanford.edu/gf/project/obs/

@@ Line 29: / Line 29: @@
 == References ==
-* [https://bmir-gforge.stanford.edu/gf/project/obs/]
+* https://bmir-gforge.stanford.edu/gf/project/obs/
 == Collaboration & Acknowledgment ==

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 MetaMap [http://mmtx.nlm.nih.gov/] is a highly powerful tool to map biomedical text to the UMLS [http://www.nlm.nih.gov/research/umls/] Metathesaurus or a custom Metathesaurus, equivalently, to discover Metathesaurus concepts referred to in text. The following article describes the way of using the Data File Builder utility inside MetaMap to build a concept recognizer for text containing NCBO terms.
-NCBO [http://www.bioontology.org/] is developing a system [http://www.bioontology.org/annotator-service] to annotate large numbers of data resources automatically, and have developed a prototype system for ontology-based annotation and indexing of biomedical data [http://www.biomedcentral.com/1471-2105/10/S9/S14]. As a part of the workflow a concept recognizer is used to recognize a given ontology concept in text. The goal of the project is to embed MetaMap into the annotator workflow. MetaMap is a very powerful for this task due to the use of complex NLP techniques in its concept recognition algorithm. Below listed is some of the useful processing done by MetaMap:
+NCBO [http://www.bioontology.org/] is developing a system [http://www.bioontology.org/annotator-service] to annotate large numbers of data resources automatically, and have developed a prototype system for ontology-based annotation and indexing of biomedical data [http://www.biomedcentral.com/1471-2105/10/S9/S14]. As a part of the workflow a concept recognizer is used to recognize a given ontology concept in text. The goal of the project is to embed MetaMap into the annotator workflow. MetaMap is a very powerful for this task due to the use of complex NLP techniques in its concept recognition algorithm.
 . Removal of problematic terms from data [numbers, single alphabets etc..]

@@ Line 1: / Line 1: @@
 == Presentation ==
-MetaMap is a highly powerful tool to map biomedical text to the UMLS Metathesaurus or a custom Metathesaurus, equivalently, to discover Metathesaurus concepts referred to in text. The following article describes the way of using the Data File Builder utility inside MetaMap to build a concept recognizer for text containing NCBO terms.
+MetaMap [http://mmtx.nlm.nih.gov/] is a highly powerful tool to map biomedical text to the UMLS [http://www.nlm.nih.gov/research/umls/] Metathesaurus or a custom Metathesaurus, equivalently, to discover Metathesaurus concepts referred to in text. The following article describes the way of using the Data File Builder utility inside MetaMap to build a concept recognizer for text containing NCBO terms.
-NCBO is developing a system to annotate large numbers of data resources automatically, and have developed a prototype system for ontology-based annotation and indexing of biomedical data [quote Nipun's paper]. As a part of the workflow a concept recognizer is used to recognize a given ontology concept in text. The goal of the project is to embed MetaMap into the annotator workflow. MetaMap is a very powerful for this task due to the use of complex NLP techniques in its concept recognition algorithm. Below listed is some of the useful processing done by MetaMap:
+NCBO [http://www.bioontology.org/] is developing a system [http://www.bioontology.org/annotator-service] to annotate large numbers of data resources automatically, and have developed a prototype system for ontology-based annotation and indexing of biomedical data [http://www.biomedcentral.com/1471-2105/10/S9/S14]. As a part of the workflow a concept recognizer is used to recognize a given ontology concept in text. The goal of the project is to embed MetaMap into the annotator workflow. MetaMap is a very powerful for this task due to the use of complex NLP techniques in its concept recognition algorithm. Below listed is some of the useful processing done by MetaMap:
 . Removal of problematic terms from data [numbers, single alphabets etc..]