| Name | Description | Language | Contact | Last Mod | Location | Limitations |
|---|---|---|---|---|---|---|
| Patient database | Semistructured patient database with structured and parsed data | XML | Stephen Johnson | March 2003 | lucid: /localprojects/pdb | deidentified data for internal department use only |
| MEDLINE | Database of citations to medical literature | XML | Stephen Johnson | March 2003 | lucid: /localprojects/medline | Available only for research purposes by Columbia staff |
| Frequency analyzer for XML files | Counts occurrences of elements in XML document | Java or Perl? | Hongfang Liu | last modified? | location? | limitations on use? |
| Medical discourse analyzer | Analysis of time, reference and other connections between events in MedLEE output | Java | Stephen Johnson | not yet available | lucid: /localprojects/tempo | internal Columbia research |
| Lifelog | surgical information on patients: vital signs, operative events, procedure, medications | XML | Greg Whalen | last modified? | location? | confidential patient information requiring IRB permission |
| Op note parser | shallow parser for operative notes | Language? | Greg Whalen | last modification? | location? | limitations for use? |
| Textbook summarizer | summarization of medical textbooks | Language? | Greg Whalen | not yet available | location? | limitations for use? |
| Enhanced SAS XML LIBNAME Engine | Tutorial for successfully importing an XML document to SAS | SAS | Jen-Hsiang Chuang | 2001 | http://www.sas.com/rnd/base/topics/sxle82/exp82/mapxmlexp.html | needs SAS 8.2 program installed |
| UMLS lexical tools | norm: normalizes a phrase (removes stop words, punctuation, etc, and alphabetizes resulting set of words. luiNorm: norm based on UMLS LUIs. wordInd: breaks up strings into a set of lowercased words | Java | Michael Cantor or Yves Lussier | early 2002 | /localprojects/ktlab/lvg2002/ | no limitations |
| MMTx | Implementation of UMLS Metamap, which analyzes phrases and maps them to UMLS terms | Java | Michael Cantor or Yves Lussier | last modified? | /localprojects/ktlab/mmtx | no limitations |
| UMLS_2002 | MRCON: contains cui, lui, sui and text of UMLS terms. MRXNS_ENG: contains lui, sui, text of normalized UMLS terms | SQL | Michael Cantor or Yves Lussier | August 2002 | /localprojects/ktlab/mysql/connect_mysql | ktlab group |
| SNOMED | tables of SNOMED concepts (normed), and concepts related to UMLS, QMR, OMIM | SQL | Michael Cantor or Yves Lussier | August 2002 | /localprojects/ktlab/mysql/connect_mysql | ktlab group |
| HGDB | tables from HGDB, a subset of OMIM published in Nature (1408 terms) | SQL | Michael Cantor or Yves Lussier | September 2002 | /localprojects/ktlab/mysql/connect_mysql | ktlab group |
| OMIM | tables from OMIM's genemap and morbid map, processed with various techniques | sql | Michael Cantor or Yves Lussier | September 2002 | /localprojects/ktlab/mysql/connect_mysql | ktlab group |
| Visualizer for MedLEE data | HTML views of MedLEE data generated with XSL and Protégé | Java? | Michael Krauthammer | last modified? | location? | limitations for use? |
| Linearizer for MedLEE data | creates in-line XML markup format for MedLEE data | Java? | Michael Krauthammer | last modified? | location? | limitations for use? |
| GENIES | information extraction from medical literature | Prolog? | Carol Friedman | last modified? | location? | limitations for use? |
| Frequency analyzer for XML files | Counts occurrences of elements in XML document | Pure Java for small data and the combination of JAVA and Perl for large collection | Hongfang Liu and Carol Friedman | last modified September 2002 | personal computer | limitations on use (Available for research purpose for staff at Columbia, seek permissions from Carol) |
| The UMLS Normalizer | Normalize UMLS including recognize and expand abbreviations (tag) | Perl (requires the UMLS and Berkley DB installed) | Hongfang Liu and Carol Friedman | last modified May 2002 | cat? | Research purpose for staff at Columbia |
| Normalized report section headings | A database for normalized report section headers (227 headers with a total of 586 header variants chosen using frequency) | Perl Hashtable | Hongfang Liu and Carol Friedman | May 2001 | leo | limitations on use (available) |
| Supervised Machine Learning Package | Naive Bayes Learning, Decision List Learning etc | Perl | Hongfang Liu and Carol Friedman | May 2002 | io | limitations on use (available ) |
| PhraseMap | Map phrase to the UMLS Concept under following four modes: Exact, Specialist-Normalized, Stemmed, Synonym replacement (Last three modes include ignoring word order and stop words.) | Perl (and Berkley DB) | Hongfang Liu and Carol Friedman | March 2002 | Cat | Not well-documented, but it is easy to use |
| PhraseGrouper | Group textual variants with the same sense | Perl (and Berkley DB) | Hongfang Liu and Carol Friedman | March 2002 | Cat | Not well-documented, but it is easy to use |
| MedLEE Linearization Tool | Merges the split MedLEE XML representation (structured and tt section) into a linearized form where the text and the semantic tags are joined together. | Java | Michael Krauthammer | July 2002 | not currently available | Some MedLEE documents won't parse yet, some linearization bugs. |
| MedLEE view generator | Generates a 'physician view' (problem list) and a 'data mining view' out of a MedLEE parsed discharge summary | Java | Michael Krauthammer | March 2001 | not currently available | Current version works with user interface. Distribution version may be working on a command line basis, but this is not implemented yet. |