| aggregator_knowledge_source |
The knowledge source that aggregated the association |
| annotation_date |
The date when the annotation was made |
| asm_score |
A composite score for comparing contig collection quality |
| association_id |
Internal (CDM) unique identifier for an association |
| attribute_cv_term_id |
If the attribute is a term from a controlled vocabulary, the ID of the term |
| attribute_name |
The attribute being captured in this annotation |
| 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... |
| checksum |
The checksum of the sequence, used to verify its integrity |
| cluster_id |
Internal (CDM) unique identifier for a cluster |
| comments |
Any comments about the association |
| 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_role |
Role(s) played by the contributor when working on the experiment |
| contributor_type |
Must be either 'Person' or 'Organization' |
| created |
Date/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_created |
Date/timestamp for when the entity was created or added to the data source |
| data_source_entity_id |
The primary ID of the entity at the data source |
| data_source_id |
Internal (CDM) unique identifier for a data source |
| data_source_updated |
Date/timestamp for when the entity was updated in the data source |
| datatype |
the rdf datatype of the value, for example, xsd:string |
| date_accessed |
The date when the data was downloaded from the data source |
| description |
Brief textual 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 |
| encoded_feature_id |
Internal (CDM) unique identifier for an encoded feature |
| 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 |
| entity_type |
Type of entity being clustered |
| 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 for an event |
| 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 |
| given_name |
The given name(s) of the contributor |
| gold_environmental_context_id |
Internal (CDM) unique identifier for a GOLD environmental context |
| has_stop_codon |
Captures whether or not the sequence includes 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-qualified URL or CURIE used as an identifier for an entity |
| is_representative |
Whether or not this member is the representative for the cluster |
| is_seed |
Whether or not this is the seed for this cluster |
| 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_value |
If the quantity describes a range, represents the upper bound of the range |
| measurement_id |
Internal (CDM) unique identifier for a measurement |
| minimum_value |
If the quantity describes a range, represents the lower bound of the range |
| mixs_environmental_context_id |
Internal (CDM) unique identifier for a mixs environmental context |
| n_contigs |
Total number of contigs |
| n_scaffolds |
Total number of scaffolds |
| name |
A string used as a name or title |
| negated |
If true, the relationship between the subject and object is negated |
| object |
Note the range of this slot is always a node |
| p_value |
The 'score' of the feature |
| participant_type |
The type of participant in the protocol |
| 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 |
| protocol_id |
Internal (CDM) unique identifier for a protocol |
| protocol_participant_id |
The unique identifier for the protocol participant |
| publication_id |
Unique identifier for a publication - e |
| quality |
The quality of the measurement, indicating the confidence that one can have i... |
| raw_value |
Raw value from the source data |
| relationship |
Relationship between this identifier and the entity in the entity_id field |
| sample_id |
Internal (CDM) unique identifier for a sample |
| 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 the clustering protocol indicating how closely a member matches t... |
| sequence |
The protein amino acid sequence |
| sequence_id |
Internal (CDM) unique identifier for a sequence |
| source |
The source for a specific piece of information; should be a CDM internal ID o... |
| 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 |
| type |
The type of the entity |
| unit |
The unit of the quantity |
| updated |
Date/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 |
| value_cv_term_id |
If the term comes from the controlled vocabulary, the CURIE for the term |
| version |
For versioned data sources, the version of the dataset |