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The PhyloAlps Project

Bibliography

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Hasnain, A., Mehmood, Q., Sana e Zainab, S., Saleem, M., Warren, C., Zehra, D., … Rebholz-Schuhmann, D. (2017). BioFed: federated query processing over life sciences linked open data. Journal of Biomedical Semantics, 8(1), 13. https://doi.org/10.1186/s13326-017-0118-0
Coissac, E., Hollingsworth, P. M., Lavergne, S., & Taberlet, P. (2016). From barcodes to genomes: extending the concept of DNA barcoding. Molecular Ecology, 25(7), 1423–1428. https://doi.org/10.1111/mec.13549
Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M. H., Bug, B., Chibucos, M. C., … Zheng, J. (2016). The Ontology for Biomedical Investigations. PloS One, 11(4), e0154556. https://doi.org/10.1371/journal.pone.0154556
ITIS. (2015). ITIS Data Model. Retrieved from https://www.itis.gov/pdf/ITIS_ConceptualModelEntityDefinition.pdf
Hinchliff, C. E., Smith, S. A., Allman, J. F., Burleigh, J. G., Chaudhary, R., Coghill, L. M., … Cranston, K. A. (2015). Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences, 112(41), 12764–12769. https://doi.org/10.1073/pnas.1423041112
Robertson, T., Döring, M., Guralnick, R., Bloom, D., Wieczorek, J., Braak, K., … Desmet, P. (2014). The GBIF Integrated Publishing Toolkit: Facilitating the Efficient Publishing of Biodiversity Data on the Internet. PLoS ONE, 9(8), e102623. https://doi.org/10.1371/journal.pone.0102623
Konstantinou, N., Spanos, D. E., & Mitrou, N. (2013). Transient and Persistent RDF Views over Relational Databases in the Context of Digital Repositories. Communications in Computer and Information Science, 390 CCIS, 342–354. https://doi.org/10.1007/978-3-319-03437-9_33
TDWG. (2013). Report of the TDWG Vocabulary Management Task Group (VoMaG). https://doi.org/10.13140/RG.2.1.1503.7920
Anguita, A., García-Remesal, M., de la Iglesia, D., & Maojo, V. (2013). NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases. BioMed Research International, 2013, 1–9. https://doi.org/10.1155/2013/983805
Federhen, S. (2012). The NCBI Taxonomy database. Nucleic Acids Research, 40(D1), 136–145. https://doi.org/10.1093/nar/gkr1178
Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R., … Vieglais, D. (2012). Darwin Core: An Evolving Community-Developed Biodiversity Data Standard. PLoS ONE, 7(1), e29715. https://doi.org/10.1371/journal.pone.0029715
Sansone, S.-A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., … Hide, W. (2012). Toward interoperable bioscience data. Nature Genetics, 44(2), 121–126. https://doi.org/10.1038/ng.1054
Gaudet, P., Bairoch, A., Field, D., Sansone, S.-A., Taylor, C., Attwood, T. K., … Yamasaki, C. (2011). Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Research, 39(Database), D7–D10. https://doi.org/10.1093/nar/gkq1173
Goff, S. A., Vaughn, M., McKay, S., Lyons, E., Stapleton, A. E., Gessler, D., … Stanzione, D. (2011). The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science, 2. https://doi.org/10.3389/fpls.2011.00034
Constable, H., Guralnick, R., Wieczorek, J., Spencer, C., & Peterson, A. T. (2010). VertNet: A New Model for Biodiversity Data Sharing. PLoS Biology, 8(2), e1000309. https://doi.org/10.1371/journal.pbio.1000309
TDWG. (2010). TDWG GUID Applicability Statement. Retrieved from https://github.com/tdwg/guid-as/blob/master/guid/applicability_statement.doc
TDWG. (2009). TDWG Life Sciences Identifiers (LSID) Applicability Statement. Retrieved from https://github.com/tdwg/guid-as/blob/master/lsid/applicability_statement.doc
Page, R. D. (2008). LSID Tester, a tool for testing Life Science Identifier resolution services. Source Code for Biology and Medicine, 3(1), 2. https://doi.org/10.1186/1751-0473-3-2
Karp, D. R., Carlin, S., Cook-Deegan, R., Ford, D. E., Geller, G., Glass, D. N., … Sugarman, J. (2008). Ethical and Practical Issues Associated with Aggregating Databases. PLoS Medicine, 5(9), e190. https://doi.org/10.1371/journal.pmed.0050190
Ratnasingham, S., & Hebert, P. D. N. (2007). BARCODING: bold: The Barcode of Life Data System. Molecular Ecology Notes, 7(3), 355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.x
Kennedy, J., Hyam, R., Kukla, R., & Paterson, T. (2006). Standard Data Model Representation for Taxonomic Information. OMICS: A Journal of Integrative Biology, 10(2), 220–230. https://doi.org/10.1089/omi.2006.10.220
Page, R. D. (2005). A Taxonomic Search Engine: Federating taxonomic databases using web services. BMC Bioinformatics, 6(1), 48. https://doi.org/10.1186/1471-2105-6-48
OMG. (2004). Life Science Identifiers Specifications. Retrieved from http://www.omg.org/cgi-bin/doc?dtc/04-05-01.pdf
TDWG. (2004). Taxonomic Concept Schema. Retrieved from http://tdwg.napier.ac.uk/doc/tdwg_tcs.pdf
National Human Genome Research Institute. (2002). Report from the NIH/NIAID/Wellcome Trust Workshop on Model Organism Databases. Retrieved from https://www.genome.gov/10006356/mod-workshop-report/
Jones, A. C., Xu, X., Pittas, N., Gray, W. A., Fiddian, N. J., White, R. J., … Brandt, S. M. (2000). SPICE: A Flexible Architecture for Integrating Autonomous Databases to Comprise a Distributed Catalogue of Life. In M. Ibrahim, J. Küng, & N. Revell (Eds.), Database and Expert Systems Applications: 11th International Conference, DEXA 2000 London, UK, September 4--8, 2000 Proceedings (pp. 981–992). Berlin, Heidelberg: Springer Berlin Heidelberg. https://doi.org/10.1007/3-540-44469-6_92