Programs--past 5+ years

Over the past 5 years or so I have designed and implemented programs to:

• Extract and edit records of interest from RxNorm and SnomedCT for use in a registry for Clinical Trials volunteers.

• Help disambiguate author names associated with PubMed articles using MeSH concept annotations. One script allows users to specify an author surname to be used to display a form containing a list of MeSH concepts associated with articles attributed to that surname, form which the user may select "canonical" full names to be used to intiate a second search for more detailed information. (For example, if we search for the author "K Cornetta" we get the results for "K", "Ken", "Kenneth" and "Kenneth G" Cornetta. Then if we decide that the author we are actually interested in is "K Cornetta" we can use the second script to find all papers listing "K Corentta" as a co-author along with a list of all authors and major MeSH annotations associated with those papers.)

• Construct and display the contents of a Network of Life Science Concepts based on the co-occurrence frequencies of MeSH concepts used to annotate the entire corpus of PubMed articles.

• Extract PubMed data from Bio2RDF and process searches for potential collaborators in Life Science research within the state of Indiana, based on MeSH terms used to annotate papers published by those researchers.

• Find or count GO categories shared by pairs of genes

• Expand gene and SNP lists using genes close to each SNP and a Protein-Protein-Interaction network, and optionally restrict expansion on the basis of hop distance to genes in the original gene list and/or cellular component co-location.

• Build transitive closures on the Gene Ontology and on the Rual-Stelzl Protein Protein Interaction network, to aid in determining subclass relationships and hop counts between nodes, respectively.

• Find and display information about user-specified SNPs and/or SNPs in a specified human chromosomal region using NCBI eUtils eSearch and eFetch.

• Retrieve NCBI sequences for genes or specified chromosomal regions

• Find endogenous repeat sequences within a sequence

• Send SQL commands directly to dbSNP via CGI, Java, and JDBC

• Get a comprehensive list of a SNP's neighbors from a local instance of dbSNP

I have also spent time exploring the Java Struts and Spring frameworks, as well as Joomla! and Drupal.