Schema Version: 1.3 Module: chado

Columns

Columns

Table Type Column Type Size Nulls Default Comments
analysisfeature Table identity float8 17 √ null

Percent identity between the locations compared. Note that these 4 metrics do not cover the full range of scores possible; it would be undesirable to list every score possible, as this should be kept extensible. instead, for non-standard scores, use the analysisprop table.
analysisfeature Table analysisfeature_id bigserial 19 nextval('companalysis.analysisfeature_analysisfeature_id_seq'::regclass)
analysisfeatureprop Table analysisfeatureprop_id bigserial 19 nextval('companalysis.analysisfeatureprop_analysisfeatureprop_id_seq'::regclass)
analysis Table sourcename varchar 255 √ null

Source name, e.g. cDNA, SwissProt.
analysisprop Table analysis_id int8 19 null
analysisprop Table analysisprop_id bigserial 19 nextval('companalysis.analysisprop_analysisprop_id_seq'::regclass)
analysis Table programversion varchar 255 null

Version description, e.g. TBLASTX 2.0MP-WashU 09-Nov-2000.
analysis_pub Table analysis_id int8 19 null
analysisfeatureprop Table type_id int8 19 null
analysis_relationship Table object_id int8 19 null

analysis_relationship.object_id is the object of the subj-predicate-obj sentence.
analysisfeature Table significance float8 17 √ null

This is some kind of expectation or probability metric, representing the probability that the analysis would appear randomly given the model. As such, any program or person querying this table can assume the following semantics: * 0 <= significance <= n, where n is a positive number, theoretically unbounded but unlikely to be more than 10 * low numbers are better than high numbers.
analysisprop Table rank int4 10 0
analysis Table name varchar 255 √ null

A way of grouping analyses. This should be a handy short identifier that can help people find an analysis they want. For instance "tRNAscan", "cDNA", "FlyPep", "SwissProt", and it should not be assumed to be unique. For instance, there may be lots of separate analyses done against a cDNA database.
analysis_relationship Table type_id int8 19 null

analysis_relationship.type_id is relationship type between subject and object. This is a cvterm, typically from the OBO relationship ontology, although other relationship types are allowed.
analysis Table algorithm varchar 255 √ null

Algorithm name, e.g. blast.
analysis Table sourceuri text 2147483647 √ null

This is an optional, permanent URL or URI for the source of the analysis. The idea is that someone could recreate the analysis directly by going to this URI and fetching the source data (e.g. the blast database, or the training model).
analysis_relationship Table subject_id int8 19 null

analysis_relationship.subject_id i s the subject of the subj-predicate-obj sentence.
analysis Table timeexecuted timestamp 29 now()
analysis Table sourceversion varchar 255 √ null
analysisfeatureprop Table rank int4 10 null
analysis_relationship Table analysis_relationship_id bigserial 19 nextval('companalysis.analysis_relationship_analysis_relationship_id_seq'::regclass)
analysisfeatureprop Table value text 2147483647 √ null
analysis_cvterm Table cvterm_id int8 19 null
analysisprop Table type_id int8 19 null
analysis_cvterm Table analysis_cvterm_id bigserial 19 nextval('companalysis.analysis_cvterm_analysis_cvterm_id_seq'::regclass)
analysis_dbxref Table dbxref_id int8 19 null
analysis_cvterm Table rank int4 10 0
analysisfeature Table normscore float8 17 √ null

This is the rawscore but semi-normalized. Complete normalization to allow comparison of features generated by different programs would be nice but too difficult. Instead the normalization should strive to enforce the following semantics: * normscores are floating point numbers >= 0, * high normscores are better than low one. For most programs, it would be sufficient to make the normscore the same as this rawscore, providing these semantics are satisfied.
analysis_relationship Table rank int4 10 0

analysis_relationship.rank is the ordering of subject analysiss with respect to the object analysis may be important where rank is used to order these; starts from zero.
analysis_cvterm Table analysis_id int8 19 null
analysisprop Table value text 2147483647 √ null
analysis_pub Table pub_id int8 19 null
analysis_cvterm Table is_not bool 1 false

If this is set to true, then this annotation is interpreted as a NEGATIVE annotation - i.e. the analysis does NOT have the specified term.
analysisfeature Table feature_id int8 19 null
analysisfeature Table rawscore float8 17 √ null

This is the native score generated by the program; for example, the bitscore generated by blast, sim4 or genscan scores. One should not assume that high is necessarily better than low.
analysisfeatureprop Table analysisfeature_id int8 19 null
analysis_pub Table analysis_pub_id bigserial 19 nextval('companalysis.analysis_pub_analysis_pub_id_seq'::regclass)
analysis_dbxref Table analysis_dbxref_id bigserial 19 nextval('companalysis.analysis_dbxref_analysis_dbxref_id_seq'::regclass)
analysis_dbxref Table analysis_id int8 19 null
analysis_dbxref Table is_current bool 1 true

True if this dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false
analysis Table analysis_id bigserial 19 nextval('companalysis.analysis_analysis_id_seq'::regclass)
analysis Table program varchar 255 null

Program name, e.g. blastx, blastp, sim4, genscan.
analysis Table description text 2147483647 √ null
analysis_relationship Table value text 2147483647 √ null

analysis_relationship.value is for additional notes or comments.
analysisfeature Table analysis_id int8 19 null