This document should be used for describing each KBase external data source in the following ways:
- How the external data source is being used in KBase, and any references to existing documentation and source code in the KBase GitHub project that describes this in more detail.
- What the license policy is of the data.
- What version or versions (if more than one copy of the data is used) are being used.
- A link or links to where the data can be accessed.
- A link or links to the documentation for this data.
ModelSEED was the basis for the biochemistry database and the metabolic model reconstruction services in KBase. The KBase biochemistry database was initially based on a reformatted load of the entire ModelSEED biochemistry database. The KBase database has subsequently undergone additional curation and manual addition of reactions from other data sources, namely published manuscripts and published metabolic models.
All data specific to ModelSEED is released under the ModelSEED Public License: https://github.com/ModelSEED/ModelSEED/blob/master/LICENSE.TXT
However, some data in the ModelSEED is derived from other sources (e.g., KEGG), and that data carries its own potential licensing restrictions.
KBase loaded the 2012 version of the ModelSEED database.
http://seed-viewer.theseed.org/seedviewer.cgi?page=ModelView
KEGG served as one data source for ModelSEED biochemistry database (see above), which forms the basis for all biochemistry in KBase. This biochemistry data is loaded into tables in the KBase central store and serves as the foundational data for all metabolic modeling services. The ModelSEED used raw ligand data reformatted from KEGG FTP dumps, adjusted for charge/pH, and loaded into our own database structures and formats. Overall, KBase includes the following specific data from KEGG:
- Molecular data from compounds found uniquely in KEGG including formula, chemical structure, and aliases
- Aliases and KEGG IDs from compounds found in multiple databases
- Stoichiometry and aliases for reactions found uniquely in KEGG
- Aliases and KEGG IDs for reactions found in multiple databases
- Coordinates for compounds and reactions from KEGG metabolic diagrams
- KEGG pathway organization for reactions found in KEGG
KEGG data was utilized for the ModelSEED project under the free academic license. No KEGG formatted data is directly accessible via KBase.
Release 62.0, April 1, 2012
IntAct is one of our primary source for the protein-protein interaction in our central store.
Creative Commons Attribution License http://www.ebi.ac.uk/intact/developer_resources
http://www.ncbi.nlm.nih.gov/geo/
GEO is the primary source of public expression data. This is what is used to populate the public KBase Expression data. This is done by the Expression service.
http://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html
"Copyright Status Unless otherwise stated, documents and files on NCBI Web servers may be freely downloaded and reproduced. However, some material on this site, such as abstracts, may be copyright protected under the U.S. and foreign copyright laws. For such material, the submitting authors or publishers retain all rights for reproduction or redistribution. Permission to reproduce these documents may be required. All persons reproducing, redistributing, or making commercial use of this information are expected to adhere to the terms and conditions asserted by the copyright holder."
Top level collection of ontologies that are used in KBase.
http://wiki.obofoundry.org/wiki/index.php/FP_001_open Creative Commons CC-BY license version 4.0 or later.
Molecular function/Cellular components/Biological process ontologies - Associated with Features. http://geneontology.org/
license - http://geneontology.org/page/use-and-license
Tissue and development ontologies - Associated with Expression Samples, GWAS. http://www.plantontology.org/
license - http://www.plantontology.org/node/279 is licensed under a Creative Commons Attribution 4.0 International License.
Environmental ontologies for plants - Associated with Expression Samples, GWAS. http://wiki.plantontology.org/index.php/Plant_Environment_Ontology_Wiki
license - http://crop.cgrb.oregonstate.edu/node/1 is licensed under a Creative Commons Attribution 3.0 United States License.
Environment Ontologies - Currently no expression data is associated with this, but it has the capability to do so. http://environmentontology.org/
license - http://environmentontology.org/home/about-envo
"We hope that the community will adopt EnvO and benefit from its potential to promote standardised data integration and access. As an open project, we welcome your use of and participation in this project. Please contact us should you like to learn more!"
Plant Metabolic Network includes all of the plant metabolic pathway databases including AraCyc, PlantCyc, BarleyCyc, BrachypodiumCyc, ChlamyCyc, CornCyc, GrapeCyc, MossCyc, OryzaCyc, PapayaCyc, PoplarCyc, SelaginellaCyc, SetariaCyc, SorghumBicolorCyc, SoyCyc, SwitchgrassCyc.
http://plantcyc.org/downloads/license_agreement.faces This license is freely available to everyone, including commercial users
http://plantcyc.org/downloads/data_downloads.faces
Plant Reactome is plant pathway database which hosts plant metabolic and regulatory pathways. Plant Reactome pathways are constructed by manual curation of pathways and reactions reported in the published literature or derived by orthology-based computational projections from curated pathways in the MetaCyc, Plant Metabolic Network, and Human Reactome databases. Pathways, reactions and gene entries in Plant Reactome are cross-referenced to many bioinformatics databases such as UniProt, ChEBI, PubChem, PubMed, Gramene and Plant Ensembl genomes and the Gene Ontology (GO).
http://plantreactome.gramene.org/copyright.html Creative Commons Attribution 3.0 United States License.
http://plants.reactome.org/about.html
The UniProt Knowledgebase (UniProtKB) provides functional information on proteins, with accurate, consistent and rich annotation. It has two sections - Swiss-Prot and TrEMBL. UniProtKB/Swiss-Prot is a high quality manually annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. UniProtKB/TrEMBL contains high quality computationally analyzed records that are enriched with automatic annotation and classification. These UniProtKB/TrEMBL unreviewed entries are kept separated from the UniProtKB/Swiss-Prot manually reviewed entries so that the high quality data of the latter is not diluted in any way.
http://www.uniprot.org/help/license Creative Commons Attribution-NoDerivs License
http://www.uniprot.org/downloads
Ensembl Plants is a joint project of EBI and Gramene. KBase uses Ensembl Plants/Gramene as a resource for plant genomes, ontology, pathway, interpro, and gene trees.
The terms of use of Ensembl data and code are summarised on the following page: http://www.ensembl.org/info/about/legal/index.html.
The EMBL-EBI terms of use also apply: http://www.ebi.ac.uk/about/terms-of-use.
Gramene terms of use is here: http://www.gramene.org/node/225
Ensembl and Gramene do not place any license restrictions on the data that they produce although they do retain copyright. Their code is explicitly licensed using the Apache v2.0 license. As noted, their databases may contain information that is subject to third-party constraints of various kinds and users of the Ensembl data and software are solely responsible for determining what these constraints are and complying with them.
Ensembl Plants: http://plants.ensembl.org/index.html Gramene: http://gramene.org/
Phytozome is the public portal to JGI's plant genome data and analysis. Currently KBase uses Phytozome as an additional resource for released plant genomes which are not available at Ensembl Plants/Gramene. Phytozome will also be used to provide diversity, expression data and many other data types to KBase in future.
Phytozome does not license or distribute any code associated with Phytozome. Phytozome is ©2006-2015 University of California Regents. All rights reserved.
Download policy is given on this link: http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10 "Some of the data available on this portal are pre-publication data and may contain errors. The goal of our policy is that early release should enable the progress of science. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by JGI and its collaborators of its comprehensive genome analysis. These restrictions will be lifted on the publication of the whole genome description or as specified on the information for each organism. During this waiting period, the data will be available for any kind of publication that does not compete directly with planned publications (e.g. reserved analyses) of the JGI and collaborators. A principal collaborator or "champion," listed in the organsim's Info page and is the point of contact and arbiter regarding publication plans. Scientists are strongly encouraged to contact the principal collaborator and JGI about their intentions and any potential collaboration. Each directory within this portal has a file describing the release policy of that data. People who access data are expected to adhere to those policies."
http://phytozome.jgi.doe.gov/pz/portal.html
Pfam is used by the Gene Families service to search for domains in genomes.
Pfam is freely available under the Creative Commons Zero ("CC0") licence. http://pfam.xfam.org/about
TIGRFAMs is used by the Gene Families service to search for domains in genomes.
Copyright 1995-2014 The J. Craig Venter Institute. All rights reserved.
This data is provided "AS IS". The J. Craig Venter Institute makes no Representation or warranty, express or implied, including without limitation any warranties of merchantability or fitness for a particular purpose, associated with the receipt or use of this data.
This database is free; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
In summary, you are free to redistribute verbatim copies of TIGRFAMs or any TIGRFAMs files in any way you like, so long as your copy of TIGRFAMs retains our copyright notice and the GNU license. You may also make modified copies of TIGRFAMs and distribute them, but your derivative database must be freely distributed under the GNU LGPL. Proprietary modification of the TIGRFAMs database is prohibited, except by a separate formal licensing agreement from the J. Craig Venter Institute.
ftp://ftp.jcvi.org/pub/data/TIGRFAMs/COPYRIGHT
http://www.jcvi.org/cgi-bin/tigrfams/index.cgi
CDD is used by the Gene Families service to search for domains in genomes. In addition to the NCBI-curated CDD domain models, we also search against CDD libraries for SMART (Simple Modular Architecture Research Tool) and for COGs (clusters of orthologous groups).
Databases of molecular data on the NCBI Web site include such examples as nucleotide sequences (GenBank), protein sequences, macromolecular structures, molecular variation, gene expression, and mapping data. They are designed to provide and encourage access within the scientific community to sources of current and comprehensive information. Therefore, NCBI itself places no restrictions on the use or distribution of the data contained therein. Nor do we accept data when the submitter has requested restrictions on reuse or redistribution. However, some submitters of the original data (or the country of origin of such data) may claim patent, copyright, or other intellectual property rights in all or a portion of the data (that has been submitted). NCBI is not in a position to assess the validity of such claims and since there is no transfer or rights from submitters to NCBI, NCBI has no rights to transfer to a third party. Therefore, NCBI cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in the molecular databases.
http://www.ncbi.nlm.nih.gov/About/disclaimer.html
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml