| affiliations |
List of organizations with which the contributor is affiliated |
| aggregator_knowledge_source |
The knowledge source that aggregated the association |
| altitude_units |
|
| altitude_value |
|
| annotation_date |
The date when the annotation was made |
| asm_score |
A composite score for comparing contig collection quality |
| association_id |
Unique identifier for an association |
| attribute_name |
The name of the attribute |
| attribute_value |
The value of the attribute |
| base |
The base URI a prefix will expand to |
| cds_phase |
For features of type CDS, the phase indicates where the next codon begins rel... |
| checkm2_completeness |
Estimate of the completeness of a contig collection (MAG or genome), estimate... |
| checkm2_contamination |
Estimate of the contamination of a contig collection (MAG or genome), estimat... |
| cluster_id |
Internal (CDM) unique identifier |
| comments |
Any comments about the association |
| conditions |
TBD |
| contig_bp |
Total size in bp of all contigs |
| contig_collection_id |
Internal (CDM) unique identifier for a contig collection |
| contig_collection_type |
The type of contig collection |
| contig_id |
Internal (CDM) unique identifier for a contig |
| contributor_id |
Internal (CDM) unique identifier for a contributor |
| contributor_roles |
List of roles played by the contributor when working on the resource |
| contributor_type |
Must be either 'Person' or 'Organization' |
| created |
POSIX timestamp for when the entity was created or added to the CDM |
| created_at |
The time at which the event started or was created |
| ctg_L50 |
Given a set of contigs, the L50 is defined as the sequence length of the shor... |
| ctg_L90 |
The L90 statistic is less than or equal to the L50 statistic; it is the lengt... |
| ctg_logsum |
The sum of the (length*log(length)) of all contigs, times some constant |
| ctg_max |
Maximum contig length |
| ctg_N50 |
Given a set of contigs, each with its own length, the N50 count is defined as... |
| ctg_N90 |
Given a set of contigs, each with its own length, the N90 count is defined as... |
| ctg_powsum |
Powersum of all contigs is the same as logsum except that it uses the sum of ... |
| data_source |
How this entity was derived and added to the database |
| datatype |
the rdf datatype of the value, for example, xsd:string |
| date_accessed |
The date when the data was downloaded from the data source |
| depth_units |
|
| depth_value |
|
| description |
Definition or description |
| doi |
The DOI for a protocol |
| e_value |
The 'score' of the feature |
| ecosystem |
JGI GOLD descriptor representing the top level ecosystem categorization |
| ecosystem_category |
JGI GOLD descriptor representing the ecosystem category |
| ecosystem_subtype |
JGI GOLD descriptor representing the subtype of ecosystem |
| ecosystem_type |
JGI GOLD descriptor representing the ecosystem type |
| elevation_units |
|
| elevation_value |
|
| encoded_by |
The feature(s) that encode this protein |
| encoded_feature_id |
Internal (CDM) unique identifier |
| end |
The start and end coordinates of the feature are given in positive 1-based in... |
| entity_id |
Internal (CDM) unique identifier for an entity in the CDM |
| entity_type |
The class of the entity |
| env_broad_scale |
Report the major environmental system the sample or specimen came from |
| env_local_scale |
Report the entity or entities which are in the sample or specimen's local vic... |
| env_medium |
Report the environmental material(s) immediately surrounding the sample or sp... |
| event_id |
Internal (CDM) unique identifier |
| evidence_for_existence |
The evidence that this protein exists |
| evidence_type |
The type of evidence supporting the association |
| experiment_id |
Internal (CDM) unique identifier for an experiment |
| family_name |
The family name(s) of the contributor |
| feature_id |
Internal (CDM) unique identifier for a feature |
| gap_pct |
The gap size percentage of all scaffolds |
| gc_avg |
The average GC content of the contig collection, expressed as a percentage |
| gc_content |
GC content of the contig, expressed as a percentage |
| gc_std |
The standard deviation of GC content across the contig collection |
| generated_by |
The algorithm or procedure that generated the feature |
| given_name |
The given name(s) of the contributor |
| gold_environmental_context |
The environmental context for this event |
| has_participant |
Participants in an experiment |
| has_stop_codon |
Captures whether or not the sequence includes a stop coordinates |
| hash |
A hash value generated from one or more object attributes that serves to ensu... |
| id |
An identifier for an element |
| identifier |
Fully-qualifier URL or CURIE used as an identifier for an entity |
| identifiers |
URIs or CURIEs used to refer to this entity |
| inputs |
The inputs for a protocol; may be software parameters, experimental reagents,... |
| language |
the human language in which the value is encoded, e |
| latitude |
|
| length |
Length of the contig in bp |
| location |
The location for this event |
| longitude |
|
| maximum_numeric_value |
|
| measurement_id |
Internal (CDM) unique identifier |
| minimum_numeric_value |
|
| mixs_environmental_context |
The environmental context for this event |
| n_contigs |
Total number of contigs |
| n_scaffolds |
Total number of scaffolds |
| name |
A string used as a name or title |
| names |
Names, alternative names, and synonyms for an entity |
| negated |
If true, the relationship between the subject and object is negated |
| numeric_value |
|
| object |
Note the range of this slot is always a node |
| organization_id |
Internal (CDM) unique identifier |
| outputs |
The outputs of a protocol; may be physical entities, files, etc |
| p_value |
The 'score' of the feature |
| part_of |
The project to which this experiment belongs |
| person_id |
Internal (CDM) unique identifier for a contributor |
| predicate |
The predicate of the statement |
| prefix |
A standardized prefix such as 'GO' or 'rdf' or 'FlyBase' |
| primary_knowledge_source |
The knowledge source that created the association |
| project_id |
Internal (CDM) unique identifier for a project |
| protein_id |
Internal (CDM) unique identifier for a protein within a cluster |
| protocol_id |
Protocol used to generate the cluster |
| protocol_participant_id |
Internal (CDM) unique identifier |
| publication_id |
Unique identifier for a publication |
| publications |
Publications that support the association |
| quality |
The quality of the measurement, indicating the confidence that one can have i... |
| raw_value |
|
| sample_id |
Internal (CDM) unique identifier |
| scaf_bp |
Total size in bp of all scaffolds |
| scaf_L50 |
Given a set of scaffolds, the L50 is defined as the sequence length of the sh... |
| scaf_L90 |
The L90 statistic is less than or equal to the L50 statistic; it is the lengt... |
| scaf_l_gt50k |
The total length of scaffolds longer than 50,000 base pairs |
| scaf_logsum |
The sum of the (length*log(length)) of all scaffolds, times some constant |
| scaf_max |
Maximum scaffold length |
| scaf_N50 |
Given a set of scaffolds, each with its own length, the N50 count is defined ... |
| scaf_N90 |
Given a set of scaffolds, each with its own length, the N90 count is defined ... |
| scaf_n_gt50K |
The number of scaffolds longer than 50,000 base pairs |
| scaf_pct_gt50K |
The percentage of the total assembly length represented by scaffolds longer t... |
| scaf_powsum |
Powersum of all scaffolds is the same as logsum except that it uses the sum o... |
| score |
Output from clustering protocol |
| sequence |
The protein amino acid sequence |
| source |
The name of the data source |
| source_database |
ID of the data source from which this entity came |
| specific_ecosystem |
JGI GOLD descriptor representing the most specific level of ecosystem categor... |
| start |
The start and end coordinates of the feature are given in positive 1-based in... |
| strand |
The strand of the feature |
| subject |
The subject of the statement |
| supporting_objects |
Objects that support the association |
| term |
|
| type |
|
| unit |
|
| updated |
POSIX timestamp for when the entity was updated in the CDM |
| url |
The URL from which the data was loaded |
| value |
Note the range of this slot is always a string |
| version |
For versioned data sources, the version of the dataset |