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RepositoryAliaslocation (url)Affiliated DatabaseInstitutional AffiliationFunding SourceDate Repository EstablishedRepository : Free Access / Paywall / MixFreeAcc/Sub CodeRequires Associated Publication for DepositAssociated Pub CodeProvides Accession Number, URI or DOIAccession Number CodeJournals Affiliated with Repository Affiliated Journals Code Type of Data Expected for Deposit State of Data at Time of DepositMutability of Deposited DataWays to cite or attribute data in Repository (text)Ways To Cite Full TextWays to Cite CodeRestrictions on DepositRestrictions textRestrictions CodeEtc
TreeBase Evolutionary Synthesis Center ( NESCentNon-profit1994Free Access1Yes1URI2American 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.1PhylogeneticsNo1Yes * 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 DataPangea 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)1995Free Access1No0Not Specified 0Earth System Science Data (ESSD), World Data Center for Marine Environmental Sciences (WDC-MARE)1Earth Systems DataYes Examples (For more info see: 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 Lithosphäre, Göttingen; Bundesamt für Kartographie und Geodäsie, Frankfurt, doi:10.1594/PANGAEA.138777) 1No0
Universal Protein ResourceUniprot 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 FELICS2002Free Access1No0DOI3No0Protein Sequences in metageNomic and environmental dataYesExamples ( 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
Toxicon 45:293-301(2005).

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 DatabaseGenbank Nucleotide Sequence Database CollaborationNCBINIH1982Free Access1No0Accession Number1No0DNA sequencingNo0No0
European Nucleotide ArchiveEBI, EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace ArchiveEMBL-European Bioinformatics Institute1981Free Access1No0Accession Number1No0Expiremental worflows around nucleotide sequencingNo0No0
RCSB Protein DataBankwwPDB, a collaborative effort with PDBe (UK), PDBj (Japan), and BMRB (USA)Brookhaven Natoional Laboratory2003Free Access1No0No 0No0Biological Macromolecular StructuresMinor 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.
YesExamples (for more information see #

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:

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 (, or can be entered in a DOI resolver (such as to automatically link to pdb4hhb.ent.gz on the main PDB ftp archive ( 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.
1Yes PDB depositions are restricted to atomic coordinates that are substantially determined by experimental measurements on actual sample specimens1
Gene Expression OmnibusGEO Access1No0Accession Number 1No0High-throughput functional geNomic data, including all array-based applications and some high-throughput sequencing data.Yes
Geochemistry of rocks of the Oceans and ContinentsGEOROC, GeoRemMax Plan InstituteDeutsche Forschungsgemeinschaft DFG2001Free Access1No0URI2No0Published chemical and isotopic data as well as extensive "metadata" for rocks, minerals and melt/fluid inclusions.No0Yesall submissions are vetted by editors1Part of earthChem GfG
World Data Center / World Data SystemWDC / WDS's National Geophysical Data CenterNGDC NoAA NESDISICSU2003Free Access1No0Not Specified 0No0Solar, geophysical and related environmental dataNo0YesData must be complete and final1
National Climtic Data CenterNCDC NoAANoAA2001Mix2No0Not Specified 0No0Weather and Climatic DataNo0No0
Durham Reaction DatabaseHEPData Univeristy UK Science and Technologiy Facilities Council 2009Free Access1No0Not Specified 0No0Total and differential cross sections, structure functions, fragmentation functions, distribuitions of jet measures, polarisations, etc... from a wide range of interactionsNo0YesPostscript 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 SystemIT IS (taxonomy) And Canada Gov Agencies ( )2009Free Access1No0Accession Number 1No0Species names and their hierarchical classificationYes ( 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,
National Center for Ecological Analysis and SynthesisNEAS DR Santa BarbraNSF2007Free Access1No0Not Specified0No0BiocomplexityNo0No0
Dryad and UNC, DUKE, NCSUNSF & IMLS2009Free Access1Yes1Accession number? 1American 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 Biologists1evolutionary biology and ecologyYesWhen 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:

1. Author(s)
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

For example:

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.
1YesYes (
Oak Ridge National Laboratory Distributed Active Archive CenteORNL DAAC Science Data and Information System (ESDIS) Project, NASA EOSDISNASA EOSDISNAFree Access1No0Not Specified0No0data 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.No0No0
EarthChem, NAVDAT, and GEOROC.Lamont-Doherty Earth Observatory (LDEO) University of Kansas, GfGNSF2003Free Access1No0Not Specified0No0No0No0All 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, NESISBoise State UniverstiyNSF2006Free Access1No0Not Specified0No0Data and metadata types for stratigraphic-based data derived from stratigraphic sections, drill holes, field, and laboratory studiesNo0No0
SedDB: Geochemistry of marine sediments from across the, PaleoStratLamont-Doherty Earth Observatory, Oregon State University, Boston University, and Boise State UniversityNSF2005Free Access1No0Not Specified0No0Compilation of geochemistry of marine and continental sedimentsNo0YesIf 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, GEOROCUniversity of KansasNSF and Geothermal Program Office of the China Lake Naval Air Weapons StationFree Access1No0Not Specified0No0Existing age, chemical, and isotopic data from Late Cretaceous to Holocene extrusive and intrusive igneous rocks from the western United States, British Columbia, and Northern MexicoNo0YesYes, Only registered users can submit data, which aids in quality control of the data.1
MGDS: Marine Geoscience Data System – MARGINS data portalMGDS Access1No0Not Specified0No0Marine geoscience data collected throughout the global oceanNo0YesYes, MARGINS and Range 2000 funded researchers must submit.1
CHRONOS: Earth history data portalCHRONOS ServiceNSF2005Free Access1No0Not Specified0No0Global federation of Earth history databases, tools, and servicesYes Examples ( : 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:

Entire System:
CHRONOS System [online]. Available from World Wide Web: (DATE WHEN SYSTEM WAS ACCESSED).

Data from multiple databases in the CHRONOS System:
CHRONOS System [online]; generated by USERNAME; using CHRONOS XML searches;; <dataset GUID> (DATE WHEN DATASET WAS ACCESSED).

Data from Neptune database:
Neptune [online]; generated by USERNAME; using CHRONOS XML searches;; 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

The US Census Bureau citing Dynamically Generated Tables/Files-

Emory University Electronic Data Center and
GEON: Geosciences Network – data and toolsGEON Access1No0Not Specified0No0Standard 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.No0No0
Petrological Database of the Ocean FloorPetDB Access1No0DOI2No0Major 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
Cambridge Structural DatabaseCCDC UniversityNon-Profit2004Free Access1Yes 1Accession Number 1No0Crystolography 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"
1YesYes, Items must be submitted as CIF1
PubChem Access1No0Not Specified0No0Chem StructuresNo0No0