1 Hierarchies and Relationships

1.7 Namespaces

2 XML Semantics

2.3 XML Schema

http://asn1.elibel.tm.fr

4 The Semantic Web and Bioinformatics Applications

4.1 The Semantic Web in Bioinformatics

http://kinasedb.ontology.ims.u-tokyo.ac.jp

5 Survey of Ontologies in Bioinformatics

5.1 Bio-Ontologies

http://img.cs.man.ac.uk/tambis is no longer valid.

http://imgproj.cs.man.ac.uk/tambis/BabyTao-new.owl is no longer valid.

5.2 Ontology Languages in Bioinformatics

http://www.bsml.org

http://www.rdcormia.com/COIN78/files/XML_Finals/\\

http://BIOML/Pages/BIOML.htm

http://www.sbw-sbml.org

http://www.mged.org

http://www.cellml.org

http://www-lbit.iro.umontreal.ca/rnaml

http://www.animorphics.net/lifesci.html

http://www.xml-cml.org

http://www.fruitfly.org/comparative

http://motifml.org

http://www.neuroml.org/main.html is now http://www.neuroml.org/.

5.3 Macromolecular Sequence Databases

5.3.1 Nucleotide Sequence Databases

http://www.ncbi.nlm.nih.gov/Genbank

http://www.ebi.ac.uk/embl

http://www.ddbj.nig.ac.jp

ftp://ftp.ddbj.nig.ac.jp/database/ddbj/xml/DDBJXML.dtd is now http://getentry.ddbj.nig.ac.jp/xml/DDBJXML.dtd.

5.3.2 Protein Sequence Databases

http://au.expasy.org/sprot

http://www.uniprot.org/support/docs/uniprot.xsd

ftp://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.xml.gz

5.4 Structural Databases

5.4.1 Nucleotide Structure Databases

http://ndbserver.rutgers.edu

5.4.2 Protein Structure Databases

http://www.sanger.ac.uk/Software/Pfam

http://smart.embl.de

http://www.expasy.org/prosite

http://blocks.fhcrc.org

http://www.ncbi.nlm.nih.gov/COG

http://umber.sbs.man.ac.uk/dbbrowser/PRINTS

http://protein.toulouse.inra.fr/prodom/\\

http://current/html/home.php

http://www.tigr.org/TIGRFAMs/

http://www.rcsb.org/pdb

http://pdb.rutgers.edu/het_dictionary.txt

http://deposit.pdb.org/pdbML/pdbx-v1.000.xsd

http://deposit.pdb.org/mmcif/

http://scop.mrc-lmb.cam.ac.uk/scop

http://www.biochem.ucl.ac.uk/bsm/cath_new

http://www.embl-ebi.ac.uk/dali

http://rebase.neb.com/rebase/rebase.html

http://mips.gsf.de

http://dip.doe-mbi.ucla.edu

http://genome.jouy.inra.fr/cgi-bin/spid/index.cgi

http://160.80.34.4/mint/

http://wilab.inha.ac.kr/hpid/

5.5 Transcription Factor Databases

http://transfac.gbf.de

http://www.bionet.nsc.ru/trrd

http://compel.bionet.nsc.ru

http://www.ifti.org/ootfd

5.6 Species-Specific Databases

http://www.yeastgenome.org

http://flybase.bio.indiana.edu

http://www.informatics.jax.org

http://gdbwww.gdb.org

http://www.pathbase.net

5.7 Specialized Protein Databases

http://senselab.med.yale.edu/senselab/ordb

http://smi-web.stanford.edu/projects/helix/riboweb.html is now http://helix-web.stanford.edu/riboweb.html.

5.8 Gene Expression Databases

5.8.1 Transcriptomics Databases

http://www.ncbi.nlm.nih.gov/dbEST/

http://bioinformatics.weizmann.ac.il/cards

http://organogenesis.ucsd.edu is no longer valid.

http://bite-it.helsinki.fi

http://www.informatics.jax.org

http://www.cage.wbmei.jhu.edu is no longer valid.

http://expression.gnf.org/cgi-bin/index.cgi

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=geo

http://cged.hgc.jp/cgi-bin/input.cgi

http://www.yeastgenome.org

http://nematode.lab.nig.ac.jp

http://www.wormbase.org

http://plasmodb.org

http://zfin.org

5.8.2 Proteomics Databases

http://userpage.chemie.fu-berlin.de/~pleiss/dhzb.html

http://www.mdc-berlin.de/~emu/heart

http://au.expasy.org/ch2d

http://www.bio-mol.unisi.it/2d/2d.html

http://us.expasy.org/ch2d/2d-index.html

http://www.pmma.pmfhk.cz

http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d

http://www.expasy.org/cgi-bin/dbxref?HSC-2DPAGE

http://www-lecb.ncifcrf.gov/phosphoDB

http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi

http://biocadmin.otago.ac.nz/tooth/home.htm

http://babbage.csc.ucm.es/2d/2d.html

http://www.abdn.ac.uk/fishprom/index.shtml

5.9 Pathway Databases

http://www.biopax.org/

http://www.genome.ad.jp/kegg

http://ecocyc.org

http://metacyc.org/

5.10 Single Nucleotide Polymorphisms

http://hgvbase.cgb.ki.se/

http://www.ncbi.nlm.nih.gov/SNP

ftp://ftp.ncbi.nlm.nih.gov/snp/specs/genoex.xsd

http://hgvbase.cgb.ki.se/

ftp://ftp.ebi.ac.uk/pub/databases/variantdbs/hgbase/hgvbase.dtd

http://www.ensembl.org/

http://snp500cancer.nci.nih.gov

http://pga.mbt.washington.edu

http://www.genome.utah.edu/genesnps

http://snp.cshl.org

http://www.hapmap.org

http://www.hapmap.org/xml-schema/2003-11-04/hapmap.xsd

6 Information Retrieval

6.3 Using Ontologies for Formulating Queries

http://www.semantxls.com

6.6 Retrieval of Knowledge Representations

http://www.semantxls.com

7 Sequence Similarity Searching Tools

7.1 Basic Concepts

ftp://ftp.ncbi.nlm.nih.gov/blast/matrices

7.3 FASTA

http://www.ebi.ac.uk/fasta33

7.4 BLAST

7.4.1 The BLAST Algorithm

http://www.ncbi.nlm.nih.gov/blast

http://blast.wustl.edu

7.4.2 BLAST Search Types

http://www.ncbi.nlm.nih.gov/blast/

http://bioinformatics.fccc.edu/software/OpenSource/beoblast/beoblast.shtml

7.4.4 BLAST Variants

http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html

http://bioinfo.bgu.ac.il/blast/psiblast_cs.html

http://www.ebi.ac.uk/blast2

http://www.ncbi.nlm.nih.gov/blast/mmtrace.shtml

http://www.ncbi.nlm.nih.gov/blast/tracemb.shtml

http://genopole.toulouse.inra.fr/blast/rpsblast.html