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Analyses of microbiome data within MGnify

METPO (Microbial Ecophysiological Trait and Phenotype Ontology) provides standardized terms for describing microbial phenotypes, growth characteristics, and culture conditions. It includes classes for growth media, temperature tolerances, pH tolerances, and relationships like "grows in" and "does not grow in".

A subspace of Metabolic Atlas for reactions.

A subspace of Metabolic Atlas for compartment-specific records for metabolites.

A resource for exploring metabolism, starting with a set of of community-curated genome-scale metabolic models of human and model organisms, enriched with pathway maps and other tools for easy browsing and analysis.

MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data. MetaCyc is [curated](http://www.biocyc.org/glossary.shtml?sid=biocyc14-3908554027#Curation) from the scientific experimental literature according to an [extensive process](https://metacyc.org/MetaCycUserGuide.shtml#TAG:__tex2page_sec_4)]. The majority of pathways occurring in it are from microorganisms and plants. MetaCyc stores thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number

Medical Subject Headings vocabulary is the set of predicates used in the MeSH RDF dump

Online Dictionary

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

Chemical reactions in the Merck Index. This website doesn't exist anymore

A semantic space of small molecules

The midlevel energy ontology (MENO) is a BFO-based midlevel ontology. It comprises the concepts for energy qualities, energy-based dispositions and energy-driven transformation and transfer processes and their interrelations. It has the goal to provide an upper level structure for these concepts for energy-related domain ontologies.

The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]

The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]

The mission of MediaDive is to transform poorly structured media recipes into a standardized database. The contents of the database include mined thousands of PDF and HTML documents. To ensure the quality of the media and continous improvement of the database, we developed an internal editor interface. Experts at the DSMZ are creating new media and curating the existing media using this interface. [adapted from https://mediadive.dsmz.de/about]

This vocabulary is used internally inside MedGen to assign temporary identifiers to terms that will later get put in UMLS. Mappings between MedGen, MedGen CIDs, and UMLS can be found [here](https://ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.gz).

The MDL number contains a unique identification number for each reaction and variation. The format is RXXXnnnnnnnn. R indicates a reaction, XXX indicates which database contains the reaction record. The numeric portion, nnnnnnnn, is an 8-digit number. [wikipedia]

A controlled vocabulary to support the study of transcription in the mouse brain

Some IDs may represent experiment sets, e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011 Others represent genomic regions (specifically deep mutational scans thereof) e.g. https://www.mavedb.org/#/experiment-sets/urn:mavedb:00000011-a