colin batchelor [email protected]...
TRANSCRIPT
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Overview
Why are we doing this?The conventional text-mining paradigmHow we do it
Where text-mining and annotation could happen in future
Challenges
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Why are we doing this?
A solution looking for many problems
Enhanced reader experienceCurrent awarenessInformation retrieval (pre-indexing)
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Enhanced HTML
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Enhanced HTML
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Conventional text-mining paradigm
There is a corpus of text (PubMed abstracts, internal reports, PDFs).
There is a resource (WordNet, FrameNet, the NTU Sentiment Dictionary).
Text mining software is trained, using the resourceon subset of corpus and tested on the remainder.
This all happens after publication.
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Resources, conventionally
StaticProbably developed for a single use casePossibly inconveniently licensedDeveloped by a single institution
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The kind of resources we want
DynamicMultiple use casesOpenDeveloped by multiple institutions
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Text mining (Oscar)http://www.sciborg.org.uk/
http://oscar3-chem.sourceforge.net/
Manual QA
Enhanced HTML
Enhanced RSS
Database
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Resources we use
StaticIUPAC Gold Book
DynamicOBO biomedical ontologies, especially:
ChEBI (see The ontology, dictionary and database of chemical entities of biological interest, Christoph Steinbeck, 1550 today)
RSC ontologies (http://www.rsc.org/ontologies)
CMO, RXNO, MOP (and more to come)
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Live resource update (stage one)
Integr. Biol., 2009, doi:10.1039/b905580k
affinity chromatography (CMO:0001006)
A chromatography method where the separation is caused by differing analyte–ligand interactions.
(source: IUPAC Orange Book 9.2.1.5)
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Live resource update (stage two)
immobilized metal affinity chromatography (CMO:0002255)
A chromatography method where the separation is caused by differing analyte–ligand interactions. Proteins containing amino acids with a specific affinity for metal ions (e.g. His which has an affinity for Co and Zn ions) are retained by the column.
metal oxide affinity chromatography(CMO:0002256)
A chromatography method where the separation is caused by differing analyte–ligand interactions. Phosphorylated proteins and peptides are retained by metal oxide particles because of their affinity for the phosphate group.
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But beware of ambiguity
distribution (noun)
Does this mean:(a) Spreading something out (a process)?(b) The way something is spread out (a
quality)?
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External trackers, downloads
Name reactionshttp://rxno.googlecode.com/
Chemical methods and apparatushttp://rsc-cmo.googlecode.com/
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How do we evaluate this? (1)
Annotations to a particular ontology are a moving target.
And we can’t guarantee completeness for any given resource–corpus combination.
(Unless we build a corpus-specific resource, which is bad.)
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How do we evaluate this? (2)
Calculate inter-annotator agreement
Focus on principles independently from the actually-existing resource.
Example: EXACT vs. CLASS vs. PART.
Peter Corbett, Colin Batchelor and Ann Copestake (2008), “Pyridines, pyridine and pyridine rings”, Proc. BERBMTM08 at LREC 2008, Marrakech, Morocco.
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Compare and contrast…
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Annotation: where and when?
Pre-publication?
(by authors)
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At publication?
(by editors)
Prospect
After publication?
(by the crowd)
ChemMantis
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Authoring: Word ontology plugin
http://ucsdbiolit.codeplex.com/
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Authoring: Word chemistry plugin
http://research.microsoft.com/en-us/projects/chem4word/default.aspx
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Challenges
Open problemsChemical structures from imagesProductive identifiers for productively-named entities
Putting ChemMantis and Prospect togetherBackfile (to 1841)Microsoft Word as well as XMLName to structure conversion