PotentialResources
Potential Resources for SWAN (Semantic Web Applications in Neuromedicine).
articles
online databases
- PubMed Citations of published scientific papers, many with abstracts, over 12 millions since mid 1960s.
- Alzheimer Research ForumâPapers of the Week AD and neuro-related papers since mid 1990s, about 32,000 currently, adding about 150 a week.
- Alzheimer Research Forum-comments on papers and news 2800 text comments sent in from ARF members, many long and with references.
- Alzheimer Research Forum - AlzGene
- Alzheimer Research Forum - APP, tau, presenilin mutation tables
- Online Mendelian Inheritance in Men (OMIM)
- Entrez Nucleotide
- Entrez Protein
- Entrez Structure
- Human Protein Reference Database
- Alzheimer Disease Mutation Database - APP, PS1, and PS2
- BIND (Biomolecular Interaction Network Database)
- KEGG Pathway Maps
- Ingenuity Pathway Analysis and Pathway Knowledgbase (subscription-based)
- ProteinLounge (subscription-based)
- The Molecular Biology Database Collection: 2005 update - list of 719 publicly accessible databases
- EMBL Nucleotide Sequence Database (also known as EMBL-Bank)
- ArrayExpress: a public repository for microarray data
ontologies & controlled vocabularies
- MeSH (Medical Subject Headings)
- GO (Gene Ontology)
- Snomed (Systematized Nomenclature of Medicine)
- Unified Medical Language System (UMLS) See also Semantic Knowledge Representation effort on UMLS
- UniProt/Swiss-Prot Term list for proteins
software tools
- Cytoscape
- Cognia Molecular
- Biocarta
- Free Mind (mind mapping)
- Telemakus
- Scientific Annotation Middleware
- Textpresso: An information retrieval and extraction system for biological literature, initial focus C. elegans
- Whatizit - link to abbreviations, protein definitions etc. The LocusLink results seem bizarre
- Critical Assessment of Information Extraction systems in Biology: Comparison of methods in text data mining community applied to biology
- JNLPBA: Joint Workshop on Natural Language Processing in Biomedicine and its Applications