The ModelSEED Biochemistry Database is found in this directory.
There are quite a few files kept together in this directory and its sub-directories, and we will describe here the most relevant ones.
The main biochemical data that we use, visualize, and serve, are in this directory and consists of two sets of files, for compounds and reactions, in two different formats:
compounds.tsvcompounds.jsonreactions.tsvreactions.json
We cover the fields we use to describe the biochemistry in the COMPOUNDS.md and REACTIONS.md files respectively.
The TSV files are in currently the master files, and the JSON files are created from the data in the TSV files on the fly. This is an important point because, at this present time, if you edit the JSON files, and then use our scripts to manage the database, you will lose your changes. We'd like to make the point that users should use our scripts, or write custom scripts that uses our python library to interface with the data in the TSV files to avoid any confusion.
All the scripts that we use to manage our data can be found in the
../Scripts directory, and there are many examples of what you can do
with the data. The underlying python library, that loads the data as
dictionaries for manipulation, can be found in
../Libs/Python/BiochemPy.
We have collected and grouped data that underlies our construction of the ModelSEED Biochemistry Database into these folders
All of the ModelSEED Biochemistry came from external sources, the majority of which comes from KEGG and MetaCyc. Here, in the Aliases directory, we link every compound and reaction to their sources.
We attempt to link and consolidate our compounds around biochemical structures, and in turn match reactions based on these structures. We also use biochemical structures for computing compound and reaction energies. In this way, we attempt to ground the core of our biochemistry on actual physical chemistry. The structures we use are downloaded from KEGG and MetaCyc and their derivatives are stored in this directory.
The results from our two different approaches to computing the compound and reaction energies are stored in this directory.
We aim to keep a list of subsystems from the ModelSEED environment as well as external sources in this directory, but we have not yet begun to maintain it.