Moore's Law. [http://en.wikipedia.org/wiki/Moore%27s_law]
DNA Sequencing Costs. [http://www.genome.gov/sequencingcosts]
Callaway E: Genome giant offers data service. Nature. 2011, 475: 435-437. 10.1038/475435a.
Article
Google Scholar
Sequence Read Archive Growth Chart. [http://www.ncbi.nlm.nih.gov/Traces/sra]
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001, 29: 365-371. 10.1038/ng1201-365.
Article
Google Scholar
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008, 26: 889-896. 10.1038/nbt.1411.
Article
Google Scholar
Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002, 30: 207-210. 10.1093/nar/30.1.207.
Article
Google Scholar
Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E: ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2011, 39: D1002-1004. 10.1093/nar/gkq1040.
Article
Google Scholar
Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P: Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010, 1 (Suppl 1): S7-10.1186/2041-1480-1-S1-S7.
Article
Google Scholar
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling sample variables with an Experimental Factor Ontology. Bioinformatics. 2010, 26: 1112-1118. 10.1093/bioinformatics/btq099.
Article
Google Scholar
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD: Logical development of the cell ontology. BMC Bioinformatics. 2011, 12: 6-10.1186/1471-2105-12-6.
Article
Google Scholar
Golbreich C, Grosjean J, Darmoni SJ: The Foundational Model of Anatomy in OWL 2 and its use. Artif Intell Med. 2013, 57: 119-132. 10.1016/j.artmed.2012.11.002.
Article
Google Scholar
Schriml LM, Arze C, Nadendla S, Chang YW, Mazaitis M, Felix V, Feng G, Kibbe WA: Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012, 40: D940-946. 10.1093/nar/gkr972.
Article
Google Scholar
Zoubarev A, Hamer KM, Keshav KD, McCarthy EL, Santos JR, Van Rossum T, McDonald C, Hall A, Wan X, Lim R: Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics. 2012, 28: 2272-2273. 10.1093/bioinformatics/bts430.
Article
Google Scholar
Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, Stegman N, Nehls G, Yost KJ, Johnson CH: CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res. 2008, 36: D892-900.
Article
Google Scholar
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004, 6: 1-6. 10.1016/S1476-5586(04)80047-2.
Article
Google Scholar
Berners-Lee T, Hendler J, Lassila O: The Semantic Web. Scientific American. 2001, 284: 34-43.
Article
Google Scholar
Antezana E, Kuiper M, Mironov V: Biological knowledge management: the emerging role of the Semantic Web technologies. Brief Bioinform. 2009, 10: 392-407. 10.1093/bib/bbp024.
Article
Google Scholar
Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J: Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008, 41: 706-716. 10.1016/j.jbi.2008.03.004.
Article
Google Scholar
Callahan A, Cruz-Toledo J, Dumontier M: Ontology-Based Querying with Bio2RDF's Linked Open Data. J Biomed Semantics. 2013, 4 (Suppl 1): S1-10.1186/2041-1480-4-S1-S1.
Article
Google Scholar
Cheung KH, Frost HR, Marshall MS, Prud'hommeaux E, Samwald M, Zhao J, Paschke A: A journey to Semantic Web query federation in the life sciences. BMC Bioinformatics. 2009, 10 (Suppl 10): S10-10.1186/1471-2105-10-S10-S10.
Article
Google Scholar
Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, Rustici G, Williams E, Parkinson H, Brazma A: Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res. 2010, 38: D690-698. 10.1093/nar/gkp936.
Article
Google Scholar
EBI RDF Platform.
Sinha AU, Merrill E, Armstrong SA, Clark TW, Das S: eXframe: reusable framework for storage, analysis and visualization of genomics experiments. BMC Bioinformatics. 2011, 12: 452-10.1186/1471-2105-12-452.
Article
Google Scholar
Drupal. [http://www.drupal.org]
Corlosquet S, Delbru R, Clark TW, Polleres A, Decker S: Produce and Consume Linked Data with Drupal. 8th International Semantic Web Conference (ISWCC) Washington DC. 2009
Google Scholar
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics. 2010, 26: 2354-2356. 10.1093/bioinformatics/btq415.
Article
Google Scholar
Gene Expression Omnibus. [http://www.ncbi.nlm.nih.gov/geo]
Dublin Core Meatadata Inititative. [http://dublincore.org]
Ciccarese P, Soiland-Reyes S, Belhajjame K, Gray A, Goble C, Clark T: PAV ontology: Provenance, Authoring and Versioning. J Biomed Semantics. 2013
Google Scholar
FOAF. [http://xmlns.com/foaf/spec]
VIVO. [http://vivoweb.org]
Bibliographic Ontology Specification. [http://bibliontology.com/specification]
NCBI Taxonomy. [http://purl.bioontology.org/ontology/NCBITAXON]
Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C: The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013, 41: D456-463. 10.1093/nar/gks1146.
Article
Google Scholar
NCI thesaurus. [http://purl.bioontology.org/ontology/NCIT]
Gremse M, Chang A, Schomburg I, Grote A, Scheer M, Ebeling C, Schomburg D: The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources. Nucleic Acids Res. 2011, 39: D507-513. 10.1093/nar/gkq968.
Article
Google Scholar
ARC RDF Classes for PHP. [https://github.com/semsol/arc2]
The R Project for Statistical Computing. [http://www.r-project.org]
BioConductor: Open source software for Bioinformatics. [http://bioconductor.org]
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5: R80-10.1186/gb-2004-5-10-r80.
Article
Google Scholar
Hoi Sui S, Merrill E, Gehlenborg N, Haseley P, Dettling M, Sytchev I, Park R, Rocca-Serra P, Corlosquet S, Gonzalez-Beltran A, Maguire E: The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework. AMIA Summits Transl Sci Proc . 2013, 2013: 70-
Google Scholar
Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R: The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res. 2012, 40: D984-991. 10.1093/nar/gkr1051.
Article
Google Scholar
Stoeckert CJ, Parkinson H: The MGED ontology: a framework for describing functional genomics experiments. Comp Funct Genomics. 2003, 4: 127-132. 10.1002/cfg.234.
Article
Google Scholar
Whetzel PL, Parkinson H, Causton HC, Fan L, Fostel J, Fragoso G, Game L, Heiskanen M, Morrison N, Rocca-Serra P: The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics. 2006, 22: 866-873. 10.1093/bioinformatics/btl005.
Article
Google Scholar
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25: 1251-1255. 10.1038/nbt1346.
Article
Google Scholar
Stem Cell Commons public SPARQL endpoint. [http://stemcellcommons.org/sparql]