@INPROCEEDINGS{HalevyDataIntegration06, author = {Halevy, Alon and Rajaraman, Anand and Ordille, Joann}, title = {Data integration: the teenage years}, booktitle = {VLDB'06.} } @inproceedings{kolaitis05, author = {Phokion Kolaitis}, title = {Schema mappings, data exchange, and metadata management}, booktitle = {Symposium on Principles of Database Systems (PODS)}, year = 2005, pages = {61-75}, } @inproceedings{GeertsKM06, author = {Floris Geerts and Anastasios Kementsietsidis and Diego Milano}, title = {MONDRIAN: Annotating and Querying Databases through Colors and Blocks}, booktitle = {Proc.\ of the Intl.\ Conf.\ on Data Engineering (ICDE)}, year = {2006}, } @INPROCEEDINGS{Reeve05SemanticAnnotation, author = {Reeve, Lawrence and Han, Hyoil}, title = {Survey of semantic annotation platforms}, booktitle = {SAC}, year = {2005}, } @inproceedings{BhagwatCTV04, author = {Deepavali Bhagwat and Laura Chiticariu and Wang Chiew Tan and Gaurav Vijayvargiya}, title = {An Annotation Management System for Relational Databases}, booktitle = {VLDB}, year = {2004}, } @inproceedings{fagin09:_clio, author = {R. Fagin and L. Haas and M. Hernandez and R. Miller and L. Popa and Y. Velegrakis}, title = {Clio: Schema Mapping Creation and Data Exchange}, Booktitle = {Conceptual Modeling: Foundations and Applications}, year = 2009, pages = {198-236}, } @article{jones_new_2006, author = {Matthew Jones and Mark Schildhauer and O. Reichman and Shawn Bowers}, journal = {Annual Review of Ecology Evolution and Systematics}, pages = {519--544}, title = {The new bioinformatics: Integrating ecological data from the gene to the biosphere}, volume = 37, year = 2006, } @inproceedings{an06:_build_seman_mappin_datab_ontol, author = {Yuan An and John Mylopoulos and Alexander Borgida}, title = {Building Semantic Mappings from Databases to Ontologies}, booktitle = {Proc.\ of the AAAI}, year = 2006, } @inproceedings{berkley09:_improv_data_discov_for_metad, author = {Chad Berkley and Shawn Bowers and Matthew Jones and Joshua Madin and Mark Schildhauer}, title = {Improving Data Discovery for Metadata Repositories through Semantic Search}, booktitle = {Proc.\ of the Intl.\ Conf.\ on Complex, Intelligent and Software Intensive Systems (CISIS)}, year = 2009, pages = {1152-1159}, } @inproceedings{mungall07:_repres_phenot_in_owl, author = {Chris Mungall}, title = {Representing Phenotypes in {OWL}}, booktitle = {Proc.\ of the Workshop on OWL: Experiences and Directions (OWLED)}, year = 2007, } @inproceedings{metacat02:_manag_heter_ecolog_data_using_morph, author = {D. Higgins and C. Berkley and M. Jones}, title = {Managing Heterogeneous Ecological Data Using {M}orpho}, booktitle = {Proc.\ of the Intl.\ Conf.\ on Scientific and Statistical Database Management (SSDBM)}, year = 2002, pages = {69-76}, } @inproceedings{berkley01:_metac, author = {C. Berkley and M. Jones and J. Bojilova and D. Higgins}, title = {Metacat: A Schema-Independent {XML} Database System}, booktitle = {Proc.\ of the Intl.\ Conf.\ on Scientific and Statistical Database Management (SSDBM)}, year = 2001, pages = {171-179}, } @article{Fegraus07, author = {E. Fegraus and S. Andelman and M. Jones and M. Schildhauer}, journal = {Bulletin of the Ecological Society of America}, number = 3, pages = {158-168}, title = {Maximizing the Value of Ecological Data with Structured Metadata: An Introduction to Ecological Metadata Language ({EML}) and Principles for Metadata Creation}, volume = 86, year = 2005, } @article{leinfelder10:_metad_driven_approac_to_loadin, author = {Ben Leinfelder and Jing Tao and Duane Costa and Matthew Jones and Mark Servilla and Margaret O'Brien and Chad Burt}, title = {A metadata-driven approach to loading and querying heterogeneous scientific data}, journal = {Ecological Informatics}, volume = 5, number = 1, year = 2010, pages = {3-8}, } @article{madin07:_ontol_for_descr_and_synth, author = {Joshua Madin and Shawn Bowers and Mark Schildhauer and Sergey Krivov and Deana Pennington and Ferdinando Villa}, title = {An ontology for describing and synthesizing ecological observation data}, journal = {Ecological Informatics}, volume = 2, number = 3, year = 2007, pages = {279-296}, } @Article{jackson01:_histor_overf_and_recen_collap, author = {{J.B.C. Jackson, \emph{et al.}}}, title = {Historical overfishing and the recent collapse of coastal ecosystems}, journal = {Science}, year = 2001, volume = 293, number = 5530, pages = {629-638}} @Article{green05:_compl_in_ecolog_and_conser, author = {{J.L. Green, \emph{et al.}}}, title = {Complexity in ecology and conservation: mathematical, statistical, and computational challenges}, journal = {BioScience}, year = 2005, volume = 55, number = 6, pages = {501-510}} @Article{worm06:_impac_of_biodiv_loss_ocean_ecosy_servic, author = {B. Worm and E. Barbier and N. Beaumont and J. Duffy and C. Folke and B. Halpern and J. Jackson and H. Lotze and F. Micheli and S. Palumbi and E. Sala and K. Selkoe and J. Stachowicz and R. Watson}, title = {Impacts of biodiversity loss on ocean ecosystem services}, journal = {Science}, year = 2006, volume = 314, number = 5800, pages = {787-790}} @inproceedings{sorokina09:_detec_inter_variab_inter_obser_ornit_data, author = {{D. Sorokina, \emph{et al.}}}, title = {Detecting and Interpreting Variable Interactions in Observational Ornithology Data}, booktitle = {ICDM Workshops}, year = 2009, pages = {64-69}, } @Article{pennings05:_do, author = {S. Pennings and C. Clark and E. Cleland and S. Collins and L. Gough and K. Gross and D. Milchunas and K. Suding}, title = {Do individual plant species show predictable responses to nitrogen addition across multiple experiments?}, journal = {Oikos}, year = 2005, volume = 110, number = 3, pages = {547-555}} @article{sidirourgos08:_colum_rdf, author = {{L. Sidirourgos, \emph{et al.}}}, title = {Column-store support for {RDF} data management: not all swans are white}, journal = {PVLDB}, volume = 1, number = 2, year = 2008, pages = {1553-1563}, } @Article{mungall110:_integ, author = {{C. Mungall, \emph{et al.}}}, title = {Integrating phenotype ontologies across multiple species}, journal = {Genome Biology}, year = 2010, volume = 11, number = {R2}} @inproceedings{he08:_graph, author = {Huahai He and Ambuj K. Singh}, title = {Graphs-at-a-time: query language and access methods for graph databases}, booktitle = {SIGMOD}, year = 2008, pages = {405-418}, } @article{chen09:_graph_olap, author = {{C. Chen, \emph{et al.}}}, title = {Graph {OLAP}: a multi-dimensional framework for graph data analysis}, journal = {Knowl. Inf. Syst.}, volume = 21, number = 1, year = 2009, } @article{ludaescher06:_scien_kepler, author = {{B. Lud{\"a}scher, \emph{et al.}}}, title = {Scientific workflow management and the Kepler system}, journal = {Conc. and Comp.: Pract. \& Exp.}, volume = 18, number = 10, year = 2006, } @InProceedings{bavoil05:_vistr, author = {{B. Bavoil, \emph{et al.}}}, title = {{VisTrails}:{E}nabling interactive multiple-view visualizations}, booktitle = {IEEE Visualization}, year = 2005 } @article{oinn04:_taver, author = {{T. Oinn, \emph{et al.}}}, title = {Taverna: {A} tool for the composition and enactment of bioinformatics workflows.}, journal = {Bioinformatics}, volume = 20, number = 17, year = 2004, } @Article{ellison06, author = {A. {Ellison,~\emph{et al}}}, title = {Analytic webs support the synthesis of ecological datasets}, journal = {Ecology}, year = 2006, volume = 87, pages = {1345--1358}} @Article{andelman04, author = {S. Andelman and C. Bowles and M. Willig and R. Waide}, title = {Understanding environmental complexity through a distributed knowledge network}, journal = {BioSciences}, year = 2004, volume = 54, number = 3, pages = {2400--246}} @inproceedings{berkley09, author = {Chad Berkley and Shawn Bowers and Matthew Jones and Joshua Madin and Mark Schildhauer}, title = {Improving Data Discovery for Metadata Repositories through Semantic Search}, booktitle = {CISIS}, year = 2009, pages = {1152-1159}, } @proceedings{baader03:_descr_logic_handb, editor = {{F. Baader, \emph{et al.}}}, title = {The Description Logic Handbook: Theory, Implementation, and Applications}, booktitle = {Description Logic Handbook}, publisher = {Cambridge University Press}, year = 2003, isbn = {0-521-78176-0}, } @Article{stevens46, author = {S. Stevens}, title = {On the theory of scales of measurement}, journal = {Science}, year = 1946, volume = 103, pages = {677--680}} @article{sheth08:_seman_sensor_web, author = {Amit P. Sheth and Cory A. Henson and Satya Sanket Sahoo}, title = {Semantic Sensor Web}, journal = {IEEE Internet Computing}, volume = 12, number = 4, year = 2008, pages = {78-83}, } @inproceedings{rector04:_owl_pizzas, author = {{A. Rector, \emph{et al.}}}, title = {{OWL Pizzas}: {P}ractical Experience of Teaching {OWL-DL}: {C}ommon Errors {\&} Common Patterns}, booktitle = {EKAW}, year = 2004, pages = {63-81}, } @inproceedings{bowers08, author = {Shawn Bowers and Joshua Madin and Mark Schildhauer}, title = {A Conceptual Modeling Framework for Expressing Observational Data Semantics}, booktitle = {Proc.\ of the Intl.\ Conf.\ on Conceptual Modeling (ER)}, pages = {41-54}, year = 2008, } @Article{balhoff10:_phenex, author = {{J. Balhoff, \emph{et al.}}}, title = {Phenex: {O}ntological Annotation of Phenotypic Diversity}, journal = {PLoS ONE}, year = 2010, volume = 5 } @article{cushing07:_compon_based_end_user_datab, author = {{J. Cushing, \emph{et al.}}}, title = {Component-based end-user database design for ecologists}, journal = {J. Intell. Inf. Syst.}, volume = 29, number = 1, year = 2007, pages = {7-24}, } @Unpublished{tarboton07:_cuahs_commun_obser_data_model, author = {D. Tarboton and J. Horsburgh and D. Maidment}, title = {{CUAHSI} Community Observations Data Model ({ODM}), Version 1.0 Design Specifications}, note = {\url{http://water.usu.edu/cuahsi/odm/}} } @Misc{sweet, title = {{Semantic Web for Earth and Environmental Terminology (SWEET)}}, note = {\url{http://sweet.jpl.nasa.gov/sweet/}}, } @Unpublished{raskin04:_enabl_seman_inter_for_earth_scien_data, author = {R. Raskin}, title = {Enabling Semantic Interoperability for Earth Science Data}, note = {\url{http://sweet.jpl.nasa.gov}}, year = 2004} @Article{fox09:_ontol, author = {P. Fox and D. McGuinness and L. Cinquini and P. West and J. Garcia and J. Benedict and D. Middleton}, title = {Ontology-supported scientific data frameworks: {T}he virtual solar-terrestrial observatory experience}, journal = {Computers \& Geosciences}, year = 2009, volume = 35, number = 4, pages = {724--738}} @ARTICLE{obsdatasearch09, author = {Anton G\"{u}ntsc and Niels Hoffmann and Patricia Kelbert and Walter Berendsohn}, title = {Effectively Searching Specimen and Observation Data with {TOQE}, the Thesaurus Optimized Query Expander}, journal = {Biodiversity Informatics}, year = {2009}, volume = {6}, pages = {53--58}, } @MISC{knb, title = {{The Knowledge Network for Biocomplexity (KNB)}}, note = {\url{http://knb.ecoinformatics.org/index.jsp}}, } @MISC{obo, title = {The OBO Foundry}, note = {\url{http://www.obofoundry.org/}}, } @Misc{om, author = {{OGC}}, title = {{The OpenGIS Observations and Measurements Encoding Standard (O\&M)}}, note = {\url{http://www.opengeospatial.org/standards/om}} } @Misc{netcdf, author = {{Unidata}}, title = {{network Common Data Form (netCDF)}}, note = {\url{http://www.unidata.ucar.edu/software/netcdf/}} } @misc{sonet, Date-Added = {2011-06-04 15:26:55 -0700}, Date-Modified = {2011-06-04 15:27:43 -0700}, Note = {\url{http://sonet.ecoinformatics.org/}}, Title = {{SONet: Scientific Observations Network}} } @misc{pellet, Author = {Clark and Parisa}, Date-Added = {2011-06-04 14:05:25 -0700}, Date-Modified = {2011-06-04 15:59:08 -0700}, Note = {\url{http://clarkparsia.com/pellet/}}, Title = {{Pellet: OWL 2 Reasoner for Java}} } @misc{owlapi, Date-Added = {2011-06-04 14:04:25 -0700}, Date-Modified = {2011-06-04 14:04:53 -0700}, Note = {\url{http://owlapi.sourceforge.net/}}, Title = {{The OWL API}} } @misc{owldl, Date-Added = {2011-07-29 14:52:00 -0700}, Date-Modified = {2011-07-29 14:52:00 -0700}, Note = {\url{http://www.w3.org/TR/owl2-overview/}}, Title = {{OWL DL}} }