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 |