|Repository||Alias||location (url)||Affiliated Database||Institutional Affiliation||Funding Source||Date Repository Established||Repository : Free Access / Paywall / Mix||FreeAcc/Sub Code||Requires Associated Publication for Deposit||Associated Pub Code||Provides Accession Number, URI or DOI||Accession Number Code||Journals Affiliated with Repository||Affiliated Journals Code||Type of Data Expected for Deposit||State of Data at Time of Deposit||Mutability of Deposited Data||Ways to cite or attribute data in Repository (text)||Ways To Cite Full Text||Ways to Cite Code||Restrictions on Deposit||Restrictions text||Restrictions Code||Etc|
|TreeBase||http://www.treebase.org/||National Evolutionary Synthesis Center ( NESCent||Non-profit||1994||Free Access||1||Yes||1||URI||2||American Journal of Botany; Annals of the Missouri Botanical Garden; Biological Journal of the Linnean Society; BMC Evolutionary Biology; Canadian Journal of Botany; Cladistics; Fungal Diversity; International Journal of Plant Sciences; Journal of Phycology; Molecular Biology and Evolution; Molecular Ecology; Molecular Phylogenetics and Evolution; Plant Systematics and Evolution; Proceeding of the National Academy of Sciences of the United States of America; Proceedings of the Royal Society B; Taxon; Zootaxa, evolution, fungal biology, Invertebrate Systematics, Mycologia, Mycological Progress, Mycological Research, MycoScience, Mycosphere online: Journal of Fungal Biology, Organisms, Diversity and Evolution. Persoonia, APS Phytopathology, APS Plant Disease, Rhodora, Muelleria, Studies in Mycology, Systematic Biology, Systematic Botany, Tropical Bryology.||1||Phylogenetics||No||1||Yes||* The paper must be published in a peer-reviewed journal or book. Data for manuscripts that are "accepted with miNor revision," "accepted," or "in press" can be published in TreeBASE. Data for manuscripts that are "submitted" or "in preparation" must Not move beyond the initial "in progress" stage of TreeBASE submission.|
* The names of all authors listed with the paper must be included.
* At least one data matrix must be included.
* At least one tree must result from an analysis of one or more data matrices. TreeBASE does Not accept matrices that were Not analyzed to produce a tree or trees for which the matrices used to produce them are Not available.
* Normally the trees should be limited to those that were published as figures in the manuscript. However, a set of trees that were used to produce a published consensus tree is also acceptable.
* Only matrices and trees listed with an analysis will ultimately become available to the public. In other words, matrices or trees must Not be orphaned but instead must be either the inputs or outputs of explicit analyses.
|Publishing Network for Geoscientific and Environmental Data||Pangea||http://www.pangaea.de/||Alfred Wegener Institute for Polar and Marine Research, and Center for Marine Environmental Sciences (University of Bremen, Germany)||The European Commission, Research, Federal Ministry of Education and Research (BMBF), Deutsche Forschungsgemeinschaft (DFG), International Ocean Drilling Program (IODP)||1995||Free Access||1||No||0||Not Specified||0||Earth System Science Data (ESSD), World Data Center for Marine Environmental Sciences (WDC-MARE)||1||Earth Systems Data||Yes||Examples (For more info see: http://wiki.pangaea.de/wiki/Citation): Bauer, Wilfried; Spaeth, G; Jacobs, Joachim; Weber, Klaus; Siegesmund, S; Thomas, RJ (2004): Geological map of BJORNNUTANE, Heimefrontfjella, Antarctica (Scale 1:25 000). Alfred Wegener Institute for Polar and Marine Research, Bremerhaven; Institut for Geologie und Dynamik der Lithosph√§re, G√∂ttingen; Bundesamt f√ºr Kartographie und Geod√§sie, Frankfurt, doi:10.1594/PANGAEA.138777)||1||No||0|
|Universal Protein Resource||Uniprot||http://www.uniprot.org/help/||UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc)||European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR).||National Institutes of Health (NIH) and European Commission (EC)'s FELICS||2002||Free Access||1||No||0||DOI||3||No||0||Protein Sequences in metageNomic and environmental data||Yes||Examples (http://www.uniprot.org/help/publications): Schneider M., Lane L., Boutet E., Lieberherr D., Tognolli M., Bougueleret L., Bairoch A.|
The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
J. Proteomics (2008).
Jungo F., Bairoch A.
Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase
Schneider M., Bairoch A., Wu C.H., Apweiler R.
Plant Protein Annotation in the UniProt Knowledgebase
Plant Physiol. 138:59-66(2005)."
|NIH Genetic Sequence Database||Genbank||http://www.ncbi.nlm.nih.gov/genbank/||International Nucleotide Sequence Database Collaboration||NCBI||NIH||1982||Free Access||1||No||0||Accession Number||1||No||0||DNA sequencing||No||0||No||0|
|European Nucleotide Archive||EBI||http://www.ebi.ac.uk/ena/about/page.php?page=about||GenBank, EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive||EMBL-European Bioinformatics Institute||1981||Free Access||1||No||0||Accession Number||1||No||0||Expiremental worflows around nucleotide sequencing||No||0||No||0|
|RCSB Protein DataBank||wwPDB||http://www.pdb.org/pdb/static.do?p=general_information/about_pdb/index.html||wwPDB, a collaborative effort with PDBe (UK), PDBj (Japan), and BMRB (USA)||Brookhaven Natoional Laboratory||2003||Free Access||1||No||0||No||0||No||0||Biological Macromolecular Structures||Minor changes may be made. These are defined as:|
* Update on header section such as citation, author's name, etc.
* Update or change on structure factor or constraint file due to format corrections or addition of data set while coordinates remain unchanged.
* Changes to chain ID, numbering, atom name, ordering of molecules and/or ligands.
A REVDAT appear in the file with a description of the change.
Major revisions to coordinates that change the structure's geometry or chemical composition (such as a change in the sequence of the polymers or ligand identity) require the entry to be obsoleted and superseded by a new deposition. The major revisions include:
* Replacement in any existing coordinates (the x,y,z values themselves).
* Changes in chemical composition (i.e. from SO4 to PO4 or SER to CYS) which change the identity of the current ligands.
* Changes in sequence such as adding or removing terminal residues.
Typically a released entry is obsoleted when the authors have collected new data or re-refined the structure. A released entry must be obsoleted by the author; it can not be withdrawn. When an entry is obsoleted, both experimental data and coordinates must be obsoleted together. Obsolete structures are still available to the public through the ftp archive. In the normal case an obsoleted structure is replaced by a new entry that receives a new PDB ID. Users who search for an obsolete structure through the main web search interface will be automatically redirected to the superceding entry.
There are some rare circumstances in which an obsolete structure is not superceded.
* The structure is incorrect, and the publication is retracted. The citation in the obsoleted entry is the published journal retraction.
* The structure is incorrect, and the entry author obsoletes the entry. The entry must contain a statement as to the reason for obsoleting the structure.
* A third-party (such as the employer) requests that the entry is obsoleted (e.g., in case of malfeasance). The citation in the obsoleted entry must be a published explanation and retraction in a peer-reviewed journal.
|Yes||Examples (for more information see http://www.pdb.org/pdb/static.do?p=general_informatioNobout_pdb/policies_references.html) #|
A PDB structure entry should be cited with its PDB ID and primary reference. For example:
PDB ID: 102L
D.W. Heinz, W.A. Baase, F.W. Dahlquist, B.W. Matthews (1993) How Amino-Acid Insertions are Allowed in an Alpha-Helix of T4 Lysozyme Nature 361:561.
An entry without a published reference can be cited with the PDB ID, author names, and title:
PDB ID: 1CI0
W. Shi, D.A. Ostrov, S.E. Gerchman, V. Graziano, H. Kycia, B. Studier, S.C. Almo, S.K. Burley, New York Structural GenomiX Research Consortium (NYSGXRC). The Structure of PNP Oxidase from S. cerevisiae
An entry may also be referenced using its Digital Object Identifier (DOI). The DOIs for PDB entries all have the same format:10.2210/pdbXXXX/pdb, where XXXX should be replaced with the desired PDB ID. The DOI can be used as part of a URL to obtain this data file (http://dx.doi.org/10.2210/pdb4hhb/pdb), or can be entered in a DOI resolver (such as http://www.crossref.org/) to automatically link to pdb4hhb.ent.gz on the main PDB ftp archive (ftp://ftp.wwpdb.org). For example, the DOI for PDB entry 4HHB is "10.2210/pdb4hhb/pdb". This links directly to the entry in the PDB file format on the FTP server.
|1||Yes||PDB depositions are restricted to atomic coordinates that are substantially determined by experimental measurements on actual sample specimens||1|
|Gene Expression Omnibus||GEO||http://www.ncbi.nlm.nih.gov/geo/info/faq.html||PubMED||NCBI||NIH||NA||Free Access||1||No||0||Accession Number||1||No||0||High-throughput functional geNomic data, including all array-based applications and some high-throughput sequencing data.||Yes||http://www.ncbi.nlm.nih.gov/geo/info/linking.html||1||No||0|
|Geochemistry of rocks of the Oceans and Continents||GEOROC||http://georoc.mpch-mainz.gwdg.de/georoc/Entry.html||EarthChem, GeoRem||Max Plan Institute||Deutsche Forschungsgemeinschaft DFG||2001||Free Access||1||No||0||URI||2||No||0||Published chemical and isotopic data as well as extensive "metadata" for rocks, minerals and melt/fluid inclusions.||No||0||Yes||all submissions are vetted by editors||1||Part of earthChem GfG|
|World Data Center / World Data System||WDC / WDS||http://www.ngdc.noaa.gov/wdc/guide/wdcguide.html||NOAA's National Geophysical Data Center||NGDC NoAA NESDIS||ICSU||2003||Free Access||1||No||0||Not Specified||0||No||0||Solar, geophysical and related environmental data||No||0||Yes||Data must be complete and final||1|
|National Climtic Data Center||NCDC||http://www.ncdc.noaa.gov/oa/about/about.html||NESDIS NoAA||NoAA||2001||Mix||2||No||0||Not Specified||0||No||0||Weather and Climatic Data||No||0||No||0|
|Durham Reaction Database||HEPData||http://durpdg.dur.ac.uk/hepdata/guide.html||Durham Univeristy||UK Science and Technologiy Facilities Council||2009||Free Access||1||No||0||Not Specified||0||No||0||Total and differential cross sections, structure functions, fragmentation functions, distribuitions of jet measures, polarisations, etc... from a wide range of interactions||No||0||Yes||Postscript and pdf figures are Not suitable. The criteria for data to be included is that it be data of a publishable form and Not preliminary data.||1|
|Interagency Taxonomic Information System||IT IS (taxonomy)||http://www.itis.gov/about_itis.html||US And Canada Gov Agencies ( http://www.itis.gov/organ.html )||2009||Free Access||1||No||0||Accession Number||1||No||0||Species names and their hierarchical classification||Yes||(http://www.itis.gov/citation.html) To cite data obtained from ITIS, the following citation format is offered as a suggestion: Retrieved [month, day, year], from the Integrated TaxoNomic Information System on-line database, http://www.itis.gov.||1||No||0|
|National Center for Ecological Analysis and Synthesis||NEAS DR||http://knb.ecoinformatics.org/knb/style/skins/nceas/index.jsp||KNB||UC Santa Barbra||NSF||2007||Free Access||1||No||0||Not Specified||0||No||0||Biocomplexity||No||0||No||0|
|Dryad||http://www.datadryad.org/about||NESCent and UNC, DUKE, NCSU||NSF & IMLS||2009||Free Access||1||Yes||1||Accession number?||1||American Society of Naturalists, European Society for Evolutionary Biology, Molecular Ecology, Molecular Phylogenetics and Evolution, Society for the Study of Evolution, Society for Integrative and Comparative Biology, Society for Molecular Biology and Evolution, and Society of Systematic Biologists||1||evolutionary biology and ecology||Yes||When using data from Dryad, please cite the original article.|
Sidlauskas, B. 2007. Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from characiform fishes. Evolution 61: 299–316.
Additionally, please cite the Dryad data package. The citation should include the following elements:
2. The article publication date
3. The name of the data file, if applicable
4. The title of the data package, which in Dryad is always "Data from: [Article name]"
5. The name "Dryad Digital Repository"
6. The data identifier
Sidlauskas, B. 2007. Data from: Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: a case study from characiform fishes. Dryad Digital Repository. doi:10.5061/dryad.20
If you are using a large number of data sources, it may be appropriate to provide a list of referenced data packages, rather than citing each individually in the references section. This list of data packages can then be deposited in Dryad, so others who read your publication can locate all of the original data.
|Oak Ridge National Laboratory Distributed Active Archive Cente||ORNL DAAC||http://daac.ornl.gov/||Earth Science Data and Information System (ESDIS) Project, NASA EOSDIS||NASA EOSDIS||NA||Free Access||1||No||0||Not Specified||0||No||0||data and information relevant to biogeochemical dynamics, ecological data, and environmental processes, critical for understanding the dynamics relating to the biological, geological, and chemical components of Earth's environment.||No||0||No||0|
|EarthChem||http://www.earthchem.org/about||PetDB, NAVDAT, and GEOROC.||Lamont-Doherty Earth Observatory (LDEO) University of Kansas, GfG||NSF||2003||Free Access||1||No||0||Not Specified||0||No||0||No||0||No||0||All NEW geochemical data used in a publication must be made available for future use by (1) submission to an accessible, persistent source such as a public database or data archive (for example, personal web sites are not persistent data archives), if it exists for the specific data type, or by (2) listing the data explicitly in a data table associated with the publication. The data must in any case be available in downloadable format.|
|Paleostrat: Paleontology and sedimentary geology||http://www.paleostrat.org/Public/about.aspx||sedDB, NESIS||Boise State Universtiy||NSF||2006||Free Access||1||No||0||Not Specified||0||No||0||Data and metadata types for stratigraphic-based data derived from stratigraphic sections, drill holes, field, and laboratory studies||No||0||No||0|
|SedDB: Geochemistry of marine sediments from across the globe.||SedDB||www.seddb.org/||earthChem, PaleoStrat||Lamont-Doherty Earth Observatory, Oregon State University, Boston University, and Boise State University||NSF||2005||Free Access||1||No||0||Not Specified||0||No||0||Compilation of geochemistry of marine and continental sediments||No||0||Yes||If your downloaded dataset was compiled from fewer than five references, we recommend including these in your article's reference list. For datasets built from a larger number of references, we recommend listing all references in electronic supplement form, if available and permitted by the publisher.||1|
|NAVDAT: Geochemistry of volcanic rocks from the western United States.||NavDAT||http://www.navdat.org/NavdatHome/FAQ.cfm#HowToSubmitData||petDB, GEOROC||University of Kansas||NSF and Geothermal Program Office of the China Lake Naval Air Weapons Station||Free Access||1||No||0||Not Specified||0||No||0||Existing age, chemical, and isotopic data from Late Cretaceous to Holocene extrusive and intrusive igneous rocks from the western United States, British Columbia, and Northern Mexico||No||0||Yes||Yes, Only registered users can submit data, which aids in quality control of the data.||1|
|MGDS: Marine Geoscience Data System ‚Äì MARGINS data portal||MGDS||http://www.marine-geo.org/about/overview.php#sec3||petDB||NSF||2003||Free Access||1||No||0||Not Specified||0||No||0||Marine geoscience data collected throughout the global ocean||No||0||Yes||Yes, MARGINS and Range 2000 funded researchers must submit.||1|
|CHRONOS: Earth history data portal||CHRONOS||http://chronos.org/faq.html#faq-N10055||Federated Service||NSF||2005||Free Access||1||No||0||Not Specified||0||No||0||Global federation of Earth history databases, tools, and services||Yes||Examples (http://www.chroNos.org/faq.html#faq-N10065) : References to material (data) from a single publication obtained through computer services like CHRONOS should be treated like first references to the original printed material except that the usual reference information is followed by the name of the service, the accession or identifying number within the service, if available, and the date when the material was accessed (Chicago Manual of Style, 2003). In our case, the service is CHRONOS. A unique GUID (Global Unique ID) is being developed for datasets in CHRONOS (CHRONOS dataset GUID).|
E.g.: Smith, J.A., 2002. Strontium isotope records of orbulinids. Journal of Electronic Publications, 34, 256-264, CHRONOS dataset <GUID> (12 November 2005).
If the data sources are multiple, a unique citation number will be provided (also a GUID, different from the dataset GUID mentioned above - under development). Suggested citations for CHRONOS and data downloaded through CHRONOS are:
CHRONOS System [online]. Available from World Wide Web: http://chronos.org (DATE WHEN SYSTEM WAS ACCESSED).
Data from multiple databases in the CHRONOS System:
CHRONOS System [online]; generated by USERNAME; using CHRONOS XML searches; http://chronos.org; <dataset GUID> (DATE WHEN DATASET WAS ACCESSED).
Data from Neptune database:
Neptune [online]; generated by USERNAME; using CHRONOS XML searches; http://services.chronos.org/databases/neptune/index.html; CHRONOS <dataset GUID> (DATE WHEN DATASET WAS ACCESSED).
For further information, please consult:
ISO 690-2, Bibliographic references, Part 2: Electronic documents or parts thereof http://www.collectionscanada.ca/iso/tc46sc9/standard/690-2e.htm#5.1
The US Census Bureau citing Dynamically Generated Tables/Files- http://www.census.gov/main/www/citation.html
Emory University Electronic Data Center http://einstein.library.emory.edu/citations_general.html and http://einstein.library.emory.edu/citing_EDC_sources.html
|GEON: Geosciences Network ‚Äì data and tools||GEON||http://www.geongrid.org/index.php/about/||SDSC||NSF||2002||Free Access||1||No||0||Not Specified||0||No||0||Standard DEM data and newer high-resolution LiDAR data, satellite imagery, street maps, geologic maps and other coverage data, Geophysical data: seismic, gravity and magnetic data, and Bore hole or well data: record of the rock types encountered at different depths at a sample location.||No||0||No||0|
|Petrological Database of the Ocean Floor||PetDB||http://www.petdb.org/contribute||earthChem||GfG||NSF||2008||Free Access||1||No||0||DOI||2||No||0||Major oxide, trace element, isotopes, age, and modal data from igneous and metamorphic rocks sampled on the ocean floor.||No||However, a list of publications citing the repository are listed at http://www.petdb.org/citations||1||No||0|
|Cambridge Structural Database||CCDC||http://www.ccdc.cam.ac.uk/products/csd/faqs/||Cambridge University||Non-Profit||2004||Free Access||1||Yes||1||Accession Number||1||No||0||Crystolography structures (In CIF packages)||Yes|| For purposes of publication |
We recommend the following footNote:
"CCDC nnnnnn contains the supplementary crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif."
|1||Yes||Yes, Items must be submitted as CIF||1|
|PubChem||http://pubchem.ncbi.nlm.nih.gov/deposit/deposit.cgi||NCBI||NIH||NA||Free Access||1||No||0||Not Specified||0||No||0||Chem Structures||No||0||No||0|