JGI MycoCosm Fungal Genomics Database
MycoCosm fungal comparative genomics database. Each fungal genome has its own schema with a common table structure for gene models, annotations, and comparative genomics. DATABASE: myco-db-1/2/3 mysql.* SCHEMA PATTERN: Each genome gets its own schema (e.g., Abobi1, Agaarg1) TABLES PER GENOME: ~100-250 KEY FUNCTIONALITY: - Gene models (FilteredModels, GeneCatalog) - Gene predictions (Genemark, Genewise) - Functional annotations (blastp, InterPro) - Secondary metabolites (SM_cluster, SM_class) - Repeat masking (RepeatMasker) - EST alignments (BlatESTclusters) - CEGMA completeness assessment EXAMPLE GENOMES: - Abobi1: Agaricus bisporus - Agaarg1: Agaricus species - Copci1: Coprinopsis cinerea
URI: https://w3id.org/jgi/mycocosm
Name: mycocosm
Classes
| Class | Description |
|---|---|
| AllModels | All gene models (filtered + unfiltered) |
| AnnotationPriority | Annotation priority settings |
| AnnotationState | Current annotation state/version |
| BlastpHit | BLASTP similarity search hit |
| BlatESTCluster | EST cluster from BLAT alignments |
| BlatESTClusterHit | Individual EST hit within a cluster |
| CEGMACompleteness | CEGMA genome completeness assessment |
| CEGMACompletenessDetail | Detailed CEGMA results per conserved gene |
| ChromInfo | Chromosome/scaffold information |
| FilteredModels | Curated/filtered gene models - the primary gene set |
| FilteredModelsBase | Base information for filtered models |
| GeneCatalog | Complete gene catalog for the genome |
| GenemarkPrediction | GeneMark ab initio gene prediction |
| GenewisePrediction | GeneWise homology-based gene prediction |
| PMAnnotationGroup | Portal management annotation group |
| PMAnnotationStatus | Annotation status in portal |
| PMAnnotator | Annotator information |
| RepeatMaskerHit | RepeatMasker repeat element hit |
| RepeatMaskerSimple | Simple repeat from RepeatMasker |
| SMClass | Secondary metabolite class |
| SMCluster | Secondary metabolite biosynthetic cluster |
| SMClusterMember | Gene member of an SM cluster |
| TransposableElement | Transposable element annotation |
| UserModel | User-submitted gene model (JAM system) |
Slots
| Slot | Description |
|---|---|
| alignment_length | |
| bitscore | |
| ceg_id | |
| cluster_id | |
| cluster_type | Type of SM cluster (NRPS, PKS, etc |
| complete_percent | Percent of complete CEGs found |
| description | |
| end | |
| est_id | |
| evalue | |
| exon_count | |
| gene_id | |
| id | |
| length | |
| model_name | |
| model_type | |
| name | Gene model name/ID |
| partial_percent | Percent of partial CEGs found |
| percent_identity | |
| priority | |
| protein_id | |
| query_id | |
| repeat_class | |
| repeat_family | |
| repeat_unit | |
| scaffold | |
| score | |
| source | |
| start | |
| state_name | |
| status | complete, partial, missing |
| strand | |
| subject_id | |
| te_class | |
| te_family | |
| timestamp | |
| total_cegs | |
| transcript_id | |
| user_id |
Enumerations
| Enumeration | Description |
|---|---|
Types
| Type | Description |
|---|---|
| Boolean | A binary (true or false) value |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| Double | A real number that conforms to the xsd:double specification |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|