Tag: microbiology

The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in ...

MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and m ...

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is appli ...

INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.

BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morph ...

BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships str ...

Norine is a platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides.

The Library of Apicomplexan Metabolic Pathways (LAMP, http://www.llamp.net) is a web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent intracellular parasites of the phylum Apicomplex ...

Shanghai RAPESEED Database: a resource for functional genomics studies of seed development and fatty acid metabolism of Brassica.

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are impo ...

BSRD is a resource for bacterial sRNA sequences with extensive annotation and expression profiles. BSRD provides combinatorial regulatory networks of transcription factors and sRNAs with their common targets. There is also a novel RNA-Seq analysis pl ...

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

Genomic data on mollicutes

BCCM/MUCL is a generalist fungal culture collection of over 30 000 filamentous fungi, yeasts and arbuscular mycorrhizal fungi including type, reference and test strains. The collections activities include the distribution of its holdings, the accessi ...

updated data repository of antimicrobial peptides | Browse, Create and Mining Antimicrobial Peptides | 157 new entries are added to in DRAMP. 33 entries are natural AMPs including 31 animal AMPs and 2 plant AMPs. 124 entries are synthetic AMPs | A br ...

MarRef is a manually curated marine microbial genome database that contains complete genomes.

Includes all non-complete marine microbial genomes regardless of the level of completeness.

MarCat is a gene (protein) catalogue of uncultivable and cultivable marine microorganisms derived from metagenomics samples.

CABRI will refine tools and test the formation of an integrated resource centre service linking catalogue databases of different organism types, genetic materials and other biologicals resources in Europe so that the user world-wide can access these ...

A Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications. Public databases for molecular typing and microbial genome diversity. A collection of open-access, curated databases that integrate popu ...

DBAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method on genomic and proteomic data.

Bacteriological, clinical, genomic and proteomic database of H. influenzae.

New Platform for the Analysis of the Molecular Impact of SARS-CoV-2 Viral Infection.

The Organonitrogen Degradation Database (ONDB) is used to catalog information about the cost, chemical properties, and biodegradation potential of commonly used organonitrogen compounds.

A database for tracking the contribution of genomics and precision health to the COVID-19 pandemic response.

BCCM/LMG is a bacterial culture collection currently comprising over 25.000 well-characterized strains. The biological origin of our collection is very broad, including bacterial isolates from food, clinical, veterinary, agricultural, aquatic and oth ...

World Data Center of Microorganisms collections

BCCM/ITM harbours one the largest and most diverse collections of well-documented mycobacteria worldwide, including the TDR TB-Strain bank. BCCM/ITM is hosted by and sharing its research interests with the Mycobacteriology Unit at the Institute of Tr ...

Deep Carbon Observatory Digital Object Registry (DCO-VIVO), is a centrally-managed digital object identification, object registration and metadata management service for the Deep Carbon Observatory. DCO-VIVO contains data, metadata, DCO-related publi ...

NHS Fife Microbiology laboratory samples and tests data.

NHS Tayside Microbiology laboratory samples and tests data.

Covering both primary and secondary care, this includes laboratory test results undertaken in NHS Lothian’s haematology, biochemistry, and microbiology labs.

A deeply phenotyped dataset of hospitalised patients undergoing an emergency or elective cholecystectomy. Longitudinal granular demographics, co-morbidities, laboratory results, physiology, medications, complications including sepsis and outcomes.

Hospitalised sepsis patients (2000-2020) by cause. Deeply phenotyped, longitudinal. Granular ethnicity and multi-morbidity. Serial acuity, physiology, blood parameters, treatments, interventions, ITU spells, outcomes, pre and post sepsis healthcare ...

ComBase is a resource for quantitative and predictive food microbiology. ComBase includes a database of observed microbial responses to a variety of food-related environments and a collection of predictive models.

The Actinobacteriophage Database.

A database of microorganisms and proteins linked to plastic biodegradation.

A webserver integrating database and prediction tools for microbe-disease associations.

A microbial strain database of manually curated CRISPR/Cas genetic manipulation system information for biomanufacturing.

Data resource collecting taxonomic composition and related metadata of > 2300 food and food-related samples. Data were produced according to a standardized pipeline and each sample is identified according the FoodEx2 classification (developed by the ...

ImitateDB is a comprehensive database for information about molecular mimicry candidates represented as DMPs and MMPs for each experimentally validated unique host pathogen protein-protein interaction.

Compilation of all names of Bacteria and Archaea which have been validly published according to the Bacteriological Code since 1. Jan. 1980, and nomenclatural changes which have been validly published since.

Construct full-length, horizontally acquired Antibiotic Resistance Genes (ARGs) from sequencing datasets. It has been designed with environmental metagenomics and microbiome experiments in mind, where the diversity and relative abundance of ARGs need ...

Retrieving contents of BacDive and related information resources in a machine-readable form. BacDive is the Bacterial Diversity Metadatabase and provides strain-linked information about bacterial and archaeal biodiversity. The web-service offers seve ...

DetR DB is a database of ionizing radiation resistance determinants contains a comprehensive catalog of radioresistant microbes and their molecular and genetic determinants of enhanced ionizing radiation tolerance. The database provides search tools ...