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Repository
Specification for the Expected Genome Content format
Basic Info
- Host: GitHub
- Owner: ggonnella
- License: other
- Default Branch: main
- Size: 21.5 KB
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- Stars: 0
- Watchers: 1
- Forks: 0
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Metadata Files
README.md
Expected Genome Content (EGC) Format Specification
Expected Genome Content (EGC) is a format for expressing rules describing expectations about the content of genomes. In its current version, it is dedicated to prokaryotic genomes, although it is possible to use it, and eventually adapt it, to eukaryotic genomes.
Structure of the format
The format is very similar in structure to GFA. Ie. it is a multi-record tabular format (with tabs as separators), where each record is introduced by a record-type (1 letter-code) in the first field.
Each record has a predetermined number of mandatory positional fields. The number, format and semantics of these fields depend on the record type.
After the positional fields, additional information can be given in the form of tags.
Differently from GFA, each line can also include a comment, i.e. a last field in the line, introduced by '#' after the tab. Everything following this character and until the end of the line is considered a comment. For simplicity, comments cannot contain tabs.
Line types
The following line types have been defined.
Groups of organisms: - 'G': (Group) a group of organisms
Genome contents: - 'U' (Units) element observed/predicted/computed in the genome sequence and/or annotation when measuring an attribute - 'M' (Model) a model in an external database identifying a unit - 'A' (Attribute) a quantity which can be measured for a genome
Rules of expectation: - 'C': (Comparison): a rule of expectation comparing a genome attribute in two group of organisms - 'V': (Value) a rule of expectation comparing a genome attribute to a value or a set of values
Sources of rules: - 'D' (Document): describe an external textual document - 'S' (Snippet): reports a snippet of text from a document - 'T' (Tables): refers to a table in a document
Metadata (these lines do not support tags): - 'X' (eXternal resources definitions): describe external resources, their usage contexts, homepage, citation and item URLs - 'Y' (tag definitions): describe user-specific tags usage contexts format and semantics
Implementation of the specification
The specification is given as a set of TextFormats specification files. The main specification file is "egc.tf.yaml", in which the "line" datatype is defined. This represent a single line (i.e. a record) of a EGC file.
Acknowledgements
This specification has been created in context of the DFG project GO 3192/1-1 “Automated characterization of microbial genomes and metagenomes by collection and verification of association rules”. The funders had no role in study design, data collection and analysis.
Owner
- Name: Giorgio Gonnella
- Login: ggonnella
- Kind: user
- Location: Goettingen, Germany
- Company: Bioinformatics, University of Goettingen
- Repositories: 36
- Profile: https://github.com/ggonnella
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| Name | Commits | |
|---|---|---|
| Giorgio Gonnella | g****a@z****e | 19 |
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