Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI''''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples)

Dbfetch is an acronym for database fetch. Dbfetch provides an easy way to retrieve entries from various databases at the EBI in a consistent manner and allows you to retrieve up to 50 entries at a time from various up-to-date biological databases. It can be used from any browser as well as well as within a web-aware scripting tool that uses wget, lynx or similar. From the browser, follow these instructions... * Select a database: If you are using the first form to paste your search items: choose a database name from this form. If you are using the second form to upload your search items: the database name is included at the beginning of each line line of the upload file followed by a colon. * Enter search terms: These MUST BE in the appropriate database format, up to 200 search items can be queried in one run. If you are using the first form: separate search items with a comma or space. If you are using the second form: separate search items with a new line. * Choose an output format: Here you can choose the simpler fasta format, or the databases'''' default format for the chosen database. * Style: You can get your results as text or html. * Retrieve! - You are now ready to fetch your results, by pressing the Retrieve button.

The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins

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THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search.

This dataset contains INSDC sequences associated with host organisms. The dataset is prepared periodically using the public ENA API (https://www.ebi.ac.uk/ena/portal/api/) using the methods described below.

EMBL-EBI also publishes other records in separate datasets (https://www.gbif.org/publisher/ada9d123-ddb4-467d-8891-806ea8d94230).

The data was then processed as follows:

1. Human sequences were excluded.

2. For non-CONTIG records, the sample accession number (when available) along with the scientific name were used to identify sequence records corresponding to the same individuals (or group of organism of the same species in the same sample). Only one record was kept for each scientific name/sample accession number.

3. Contigs and whole genome shotgun (WGS) records were added individually.

4. The records that were missing some information were excluded. Only records associated with a specimen voucher or records containing both a location AND a date were kept.

5. The records associated with the same vouchers are aggregated together.

6. A lot of records left corresponded to individual sequences or reads corresponding to the same organisms. In practise, these were "duplicate" occurrence records that weren't filtered out in STEP 2 because the sample accession sample was missing. To identify those potential duplicates, we grouped all the remaining records by `scientific_name`, `collection_date`, `location`, `country`, `identified_by`, `collected_by` and `sample_accession` (when available). Then we excluded the groups that contained more than 50 records. The rationale behind the choice of threshold is explained here: https://github.com/gbif/embl-adapter/issues/10#issuecomment-855757978

7. To improve the matching of the EBI scientific name to the GBIF backbone taxonomy, we incorporated the ENA taxonomic information. The kingdom, Phylum, Class, Order, Family, and genus were obtained from the ENA taxonomy checklist available here: http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip

More information available here: https://github.com/gbif/embl-adapter#readme

You can find the mapping used to format the EMBL data to Darwin Core Archive here: https://github.com/gbif/embl-adapter/blob/master/DATAMAPPING.md

Subscribers can find out export and import data of 23 countries by HS code or product’s name. This demo is helpful for market analysis.

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images.

Dataset of the type entry from the database PRINTS - version 42.0

Data item of the type family from the database ncbifam with accession NF000022 and name streptogramin B lyase Vgb(A)

M-CSA is a database about enzyme reaction. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of enzymes. Each record contains references about protein and structure (sequence, biological species, PDB, Catalytic CATH Domains), enzyme reaction and enzyme mechanisms. This database represents a unified resource that combines the data in both MACiE (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/) and the CSA (http://www.ebi.ac.uk/thornton-srv/databases/CSA/).

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride) is one of the main repositories of MS derived proteomics data.

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The EMBL Australia Bioinformatics Resource, located at The University of Queensland, provides an Australian-based entry to many of the data services of the European Bioinformatics Institute (EBI). The EBI is an institute within the European Molecular Biology Laboratory (EMBL) and is the world's premier life sciences data resource.

Five collections of nucleotide and protein sequences derived from Australian dwelling plants and animals (identified through the Atlas of Living Australia's instances of the Australian Faunal Directory and the Australian Plant Census) are available from within the EMBL-EBI database.

These data collections contain all current internationally published nucleotide and protein sequences derived from Australian dwelling (native and common/significant introduced (e.g. crop/weed/feral)) organisms and are structured using a taxonomical hierarchy to facilitate searching by species.

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The database of Genotypes and Phenotypes (dbGaP) was developed to archive and distribute the data and results from studies that have investigated the interaction of genotype and phenotype in Humans.

*Sorting of the chemical properties of these proteins was based on their annotations in the UniProt protein database (www.uniprot.org) and EMBL-EBI database (www.ebi.ac.uk).

ChIP-Seq data for 154 CD4-positive, alpha-beta T cell sample(s). 355 run(s), 265 experiment(s), 250 analysis(s) on human genome GRCh37. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/blueprint_Epivar/protocols/README_chipseq_analysis_ebi_20160816

This dataset contains INSDC sequences associated with environmental sample identifiers. The dataset is prepared periodically using the public ENA API (https://www.ebi.ac.uk/ena/portal/api/) by querying data with the search parameters: `environmental_sample=True & host=""`

EMBL-EBI also publishes other records in separate datasets (https://www.gbif.org/publisher/ada9d123-ddb4-467d-8891-806ea8d94230).

The data was then processed as follows:

1. Human sequences were excluded.

2. For non-CONTIG records, the sample accession number (when available) along with the scientific name were used to identify sequence records corresponding to the same individuals (or group of organism of the same species in the same sample). Only one record was kept for each scientific name/sample accession number.

3. Contigs and whole genome shotgun (WGS) records were added individually.

4. The records that were missing some information were excluded. Only records associated with a specimen voucher or records containing both a location AND a date were kept.

5. The records associated with the same vouchers are aggregated together.

6. A lot of records left corresponded to individual sequences or reads corresponding to the same organisms. In practise, these were "duplicate" occurrence records that weren't filtered out in STEP 2 because the sample accession sample was missing. To identify those potential duplicates, we grouped all the remaining records by `scientific_name`, `collection_date`, `location`, `country`, `identified_by`, `collected_by` and `sample_accession` (when available). Then we excluded the groups that contained more than 50 records. The rationale behind the choice of threshold is explained here: https://github.com/gbif/embl-adapter/issues/10#issuecomment-855757978

7. To improve the matching of the EBI scientific name to the GBIF backbone taxonomy, we incorporated the ENA taxonomic information. The kingdom, Phylum, Class, Order, Family, and genus were obtained from the ENA taxonomy checklist available here: http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip

More information available here: https://github.com/gbif/embl-adapter#readme

You can find the mapping used to format the EMBL data to Darwin Core Archive here: https://github.com/gbif/embl-adapter/blob/master/DATAMAPPING.md

To mimic a complex marine sample, a dilution series of R. pomeroyi and T. pseudonana was created at different cellular ratios. These mixtures were filtered and proteins were extracted from the filter for tryptic digestion and LC-MS/MS analysis.

Biological fractions were lysed, digested and analyzed using proteomic mass spectrometry.

Data are available for download at the EBI PRIDE Archive.
Homepage: https://www.ebi.ac.uk/pride/archive
Project URL: https://www.ebi.ac.uk/pride/archive/projects/PXD004758
Data URL: https://www.ebi.ac.uk/pride/archive/projects/PXD004758/files

Subscribers can find out export and import data of 23 countries by HS code or product’s name. This demo is helpful for market analysis.