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= Ten Simple Rules for Developing Public Biological Databases =
== Supplementary Webpage for Tools and Technologies Recommendations ==
R: Recommendation, E: Example

=== - Resources for available databases (R) ===
|| '''Resource''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| NAR 2016's Database Collection |||| NAR collection of online Molecular Biology Database 2016 |||| [[http://www.oxfordjournals.org/our_journals/nar/database/a/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/26740669|PubMed]] ||
|| Pathguide  |||| The Pathway Resource List |||| [[http://pathguide.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/16381921|PubMed]] ||
|| The Registry   |||| Collection of analytical tools and data services for bioinformatics |||| [[https://bio.tools/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/26538599|PubMed]] ||
|| The Bioinformatics Links Directory   |||| List of curated links to molecular resources, tools and databases |||| [[http://bioinformatics.ca/links_directory/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/21715385|PubMed]] ||
|| OMICtools   |||| Collection of classified omic tools |||| [[http://omictools.com/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/25024350 |PubMed]] ||
|| MetaBase   |||| A user-contributed database of biological databases |||| [[http://MetaDatabase.Org|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/22139927 |PubMed]] ||


=== - Ontologies and semantics (R) ===
|| '''Resource''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| The OBO Foundry |||| Collection of Biomedical Ontologies |||| [[http://www.obofoundry.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/17989687|PubMed]] ||

=== - File formats (E) ===
|| '''Format''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| FASTA |||| File format for representing biological sequences |||| [[http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/3162770|PubMed]] ||
|| GFF3 |||| File format for representing gene annotations  |||| [[http://www.sequenceontology.org/gff3.shtml|Link]] ||||  -- ||
|| BioPax |||| Pathway exchange language for Biological pathway data |||| [[http://www.biopax.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/20829833|PubMed]] ||
|| Extended Newick |||| Standard for representation of phylogenetic networks |||| [[http://dmi.uib.es/~gcardona/BioInfo/enewick.html|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/19077301|PubMed]] ||

=== - Biological libraries of programming languages (E) ===
|| '''Library''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' ||
|| BioJava |||| Open source project for Java tools for bioinformatics  |||| [[http://www.biojava.org|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/22877863|PubMed]] ||
|| BioPerl |||| Collection of Perl modules for  bioinformatics applications  |||| [[http://www.bioperl.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/12368254|PubMed]] ||
|| BioPython |||| Open source collection of Python tools for bioinformatics  |||| [[http://www.biopython.org|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/19304878|PubMed]] ||
|| BioJS |||| Full-featured biological workbench written in JS  |||| [[http://www.ebi.ac.uk/tools/biojs/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/25075290|PubMed]] ||
|| R Bioconductor |||| Collection of R packages provides tools for the analysis biological data  |||| [[http://www.bioconductor.org/|Link]] ||||  [[http://www.ncbi.nlm.nih.gov/pubmed/15461798|PubMed]] ||