Alkaline Phosphatase: 52 papers
By Michael Schroeder, Biotec, 2003
Effects of alkaline phosphatase and its inhibitor Levamisole…
10
GoPubMed Example
Phosphofructokinase
By Michael Schroeder, Biotec, 2003
2
GoPubMed and beyond: Rules and reasoning for ontology-based literature search
By Michael Schroeder, Biotec, 2003
3
Problem
GoPubMed and beyond:
Rules and reasoning for ontology-based literature search
Michael Schroeder
BioTechnological Center TU Dresden ms@mpi-cbg.de http://www.biotec.tu-dresden.de
In PubMed the article is listed at position 84! And hence unlikely to be read
By Michael Schroeder, Biotec, 2003
13
GoPubMed and beyond: Rules and reasoning for ontology-based literature search
By Michael Schroeder, Biotec, 2003
5
PubMed Example
A keyword search for levamisole inhibitor produces well over 100 hits in PubMed. To find out about specific functions, we have to go through all these papers! We are interested in the relevant enzymatic functions. A refined search for Levamisole inhibitor enzymatic activity produces only 5 hits - a lot of relevant papers have been dropped.
By Michael Schroeder, Biotec, 2003
16
PubMed XML Output
<PubmedArticle> <MedlineCitation Owner="NLM" Status="Publisher"> <PMID>15469972</PMID> <DateCreated> <Year>2004</Year> <Month>10</Month> <Day>7</Day> </DateCreated> <Article> <Journal> <ISSN>0950-1991</ISSN> <JournalIssue PrintYN="N"> <PubDate> <Year>2004</Year> <Month>10</Month> <Day>6</Day> </PubDate> </JournalIssue> <Coden>DEVPED</Coden> <Title>Development (Cambridge, England)</Title> <ISOAbbreviation>Development</ISOAbbreviation> </Journal>…
By Michael Schroeder, Biotec, 2003 7
Байду номын сангаас
GoPubMed Example
Let’s look for some functions: 70 papers including terms, which are enzyme activities
By Michael Schroeder, Biotec, 2003 8
By Michael Schroeder, Biotec, 2003
18
Code Snippet
%%% XML reading tests :- eval(test_xml1()).
Prolog rules Java objects
evaluate(ChildNode):"Year"=ChildNode.getNodeName(), printout(ChildNode). evaluate(ChildNode):"Initials"=ChildNode.getNodeName(), printout(ChildNode), println([**********************]). evaluate(ChildNode):"FirstName"=ChildNode.getNodeName(), printout(ChildNode). evaluate(ChildNode):"ForeName"=ChildNode.getNodeName(), printout(ChildNode). evaluate(ChildNode):"LastName"=ChildNode.getNodeName(), printout(ChildNode). evaluate(ChildNode):"ArticleTitle"=ChildNode.getNodeName(), printout(ChildNode). printout(ChildNode):ChildNodeName = ChildNode.getNodeName(), DataName = ChildNode.getFirstChild(), StringName = DataName.getNodeValue(), println([ChildNodeName, ": ",StringName]).
Offer a rule-based platform for distributed agent programming.
Expose logic and agent behaviour as rules; Access data sources via wrappers written in Java Make all Java API from available packages directly accessible from rules; Run within the Java runtime; Enable rapid prototyping of applications;
By Michael Schroeder, Biotec, 2003
17
Output
Year: 2004 ArticleTitle: Developmental potential of defined neural progenitors derived from mouse embryonic stem cells. LastName: Plachta FirstName: Nicolas Initials: N ********************** LastName: Bibel FirstName: Miriam Initials: M ********************** LastName: Tucker FirstName: Kerry Lee Initials: KL ********************** LastName: Barde FirstName: Yves-Alain Initials: YA ****************************************** Year: 2004 ArticleTitle: Eye evolution: a question of genetic promiscuity. LastName: Nilsson ForeName: Dan-E Initials: DE ********************** …
By Michael Schroeder, Biotec, 2003
14
Prova
By Michael Schroeder, Biotec, 2003
15
Prova
Rule-based Java scripting for middleware Combination of object-oriented and declarative programming
GoPubMed Example
Transferase Kinase Hydrolase Oxidoreductase Lyase
8 6 58 2 1
9
By Michael Schroeder, Biotec, 2003
GoPubMed Example
…alkaline phosphatase inhibitor levamisole…
Towards a Bioinformatics Semantic Web