# Metadata ## All objects All metadata objects support the following fields: | Field | Supported values | Description | | --------: | :---------------------------------------------------------------------------: | ------------------- | | created\* | [Date](https://manual.microbial-genomes.org/master/part1/glossary#miga-dates) | Date of creation | | updated\* | [Date](https://manual.microbial-genomes.org/master/part1/glossary#miga-dates) | Date of last update | > **\*** Mandatory ## Projects The following metadata fields are recognized by different interfaces for **Projects**: ### Project Features Metadata with additional information and features about the project: | Field | Supported values | Description | | ----------: | :---------------------------------------------------------------------------: | --------------------- | | comments | String | Free-form comments | | description | String | Free-form description | | name\* | [Name](https://manual.microbial-genomes.org/master/part1/glossary#miga-names) | Name‡ | > **\*** Mandatory ### Project System Metadata Metadata entries automatically set by MiGA: | Field | Supported values | Description | | ---------: | :--------------: | ----------------------------------------------------------------------------- | | datasets\* | Array of String | List of datasets in the project | | type\* | String | [Type](https://manual.microbial-genomes.org/master/part2/types#project-types) | > **\*** Mandatory > > **‡** By default the base name of the project path ### Project Flags Metadata entries that trigger specific behaviors in MiGA: | Field | Supported values | Description | | -------------: | :--------------: | -------------------------------------------- | | ref\_project | Path | Project with reference taxonomy | | db\_proj\_dir | Path | Directory containing database projects | | tax\_pvalue | Float \[0,1] | Max p-value to transfer taxonomy (def: 0.05) | | aai\_p | String | Value of aai.rb -p° on AAI (def: blast+) | | haai\_p | String | Value of aai.rb -p° on hAAI (def: blast+) | | ani\_p | String | Value of ani.rb -p° on ANI (def: blast+) | | max\_try | Integer | Max number of task attempts (def: 10) | | aai\_save\_rbm | Boolean | Should RBMs be saved for OGS analysis? | | ogs\_identity | Float \[0,100] | Min RBM identity for OGS (def: 80) | | clean\_ogs | Boolean | If false, keeps ABC (clades only) | | run\_clades | Boolean | Should clades be estimated from distances? | | gsp\_ani | Float \[0,100] | ANI limit to propose gsp clades (def: 90) | | gsp\_aai | Float \[0,100] | AAI limit to propose gsp clades (def: 95) | | gsp\_metric | String | Metric to propose clades: `ani` (def), `aai` | | ess\_coll | String | Collection of essential genes to use+ | | min\_qual | Float (or 'no') | Min. genome quality (or no filter; def: 25) | > **°** By default: `blast+`. Other supported values: `blast`, `blat`, `diamond` (except for ANI), and `fastani` (only for ANI), `no` (only for hAAI). If using `diamond` and/or `fastani`, the corresponding software must be installed. **Important**: These defaults will change in v1.0 to: `blast+` for hAAI, `diamond` for AAI, and `fastani` for ANI. > > **+** One of: `dupont_2012` (default), or `lee_2019` ### Project Hooks Additionally, hooks can be defined for projects as arrays of arrays containing the action name and the arguments (if any). For example, one can define: ``` on_processing_ready: [ ['run_cmd', 'date > {{project}}/ALL_DONE.txt'], ['run_cmd', 'sendmail ...'] ] ``` or ``` on_add_dataset: [ ['run_cmd', 'echo {{object}} > {{project}}/LATEST_DATASET.txt'] ] ``` Supported events: * `on_create()`: When created * `on_load()`: When loaded * `on_save()`: When saved * `on_add_dataset(object)`: When a dataset is added, with name `object` * `on_unlink_dataset(object)`: When dataset with name `object` is unlinked * `on_result_ready(object)`: When any result is ready, with key `object` * `on_result_ready_{result}()`: When `result` is ready * `on_processing_ready()`: When processing is complete Supported hooks: * `run_lambda(lambda, args...)` * `run_cmd(cmd)` ## Datasets The following metadata fields are recognized by different interfaces for **Datasets**: ### Dataset Features Metadata with additional information and features about the dataset: | Field | Supported values | Description | | ----------------: | :--------------: | --------------------------------------- | | tax | MiGA::Taxonomy | Taxonomy of the dataset | | quality | String | Description of genome quality | | dprotologue | String | Taxonumber in the Digital Protologue DB | | ncbi\_tax\_id | String | Linking ID(s)‡ for NCBI Taxonomy | | ncbi\_nuccore | String | Linking ID(s)‡ for NCBI Nucleotide | | ncbi\_asm | String | Linking ID(s)‡ for NCBI Assembly | | ebi\_embl | String | Linking ID(s)‡ for EBI EMBL | | ebi\_ena | String | Linking ID(s)‡ for EBI ENA | | web\_assembly | String | URL to download assembly | | web\_assembly\_gz | String | URL to download gzipped assembly | | see\_also | String | Link(s)‡ in the format text:url | | is\_type | Boolean | If it is type material | | is\_ref\_type | Boolean | If it is reference material° | | type\_rel | String | Relationship to type material | | suspect | Array(String) | Flags indicating a suspect dataset | > **‡** Multiple values can be provided separated by commas or colons > > **°** This is not a valid type, but it represents the closest available dataset to material that is unavailable and unlikely to ever become available. See also [Federhen, 2015, NAR](https://doi.org/10.1093/nar/gku1127) ### Dataset System Metadata Metadata entries automatically set by MiGA: | Field | Supported values | Description | | -------------: | :--------------: | ------------------------------------------------------------------------------ | | type\* | String | [Type](https://manual.microbial-genomes.org/master/part2/types#dataset-types) | | ref | Boolean | [Reference](https://manual.microbial-genomes.org/master/part2/types#reference) | | inactive | Boolean | If auto-processing should stop | | metadata\_only | Boolean | Dataset with metadata but without input data | | status | String | Proc. status: complete, incomplete, inactive | | \_step | String | For internal control of processing | | \_try\_`step` | Integer | For internal control of processing | | ~~user~~ | String | Deprecated | > **\*** Mandatory ### Dataset Flags Metadata entries that trigger specific behaviors in MiGA: | Field | Supported values | Description | | ----------: | :--------------: | -------------------------------------- | | run\_`step` | Boolean | Forces running or not `step` | | db\_project | Path | Project to use as database | | dist\_req | Array of String | Run distances against these datasets\* | > **\*** When searching best-matching datasets, include these datasets even if they are not visited using the medoid tree ### Dataset Hooks Additionally, hooks can be defined for datasets as arrays of arrays containing the action name and the arguments. See above ([project hooks](#project-hooks)) for examples. Supported events: * `on_load()`: When loaded * `on_save()`: When saved * `on_remove()`: When removed * `on_inactivate()`: When inactivated * `on_activate()`: When activated * `on_result_ready(object)`: When any result is ready, with key `object` * `on_result_ready_{result}()`: When `result` is ready * `on_preprocessing_ready()`: When preprocessing is complete Supported hooks: * `run_lambda(lambda, args...)` * `clear_run_counts()` * `run_cmd(cmd)` --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://manual.microbial-genomes.org/master/part5/metadata.md?ask= ``` The question should be specific, self-contained, and written in natural language. 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