Difference between revisions of "Chado Companalysis Module"
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Revision as of 16:10, 5 March 2007
Contents
Introduction
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Tables
Table: analysis
An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation.
| F-Key | Name | Type | Description |
|---|---|---|---|
| analysis_id | serial | PRIMARY KEY | |
| name | character varying(255) | 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. | |
| description | text | ||
| program | character varying(255) | UNIQUE#1 NOT NULL Program name, e.g. blastx, blastp, sim4, genscan. | |
| programversion | character varying(255) | UNIQUE#1 NOT NULL Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. | |
| algorithm | character varying(255) | Algorithm name, e.g. blast. | |
| sourcename | character varying(255) | UNIQUE#1 Source name, e.g. cDNA, SwissProt. | |
| sourceversion | character varying(255) | ||
| sourceuri | text | 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). | |
| timeexecuted | timestamp without time zone | NOT NULL DEFAULT ('now'::text)::timestamp(6) with time zone |
Tables referencing this one via Foreign Key Constraints:
Table: analysisfeature
Computational analyses generate features (e.g. Genscan generates transcripts and exons; sim4 alignments generate similarity/match features). analysisfeatures are stored using the feature table from the sequence module. The analysisfeature table is used to decorate these features, with analysis specific attributes. A feature is an analysisfeature if and only if there is a corresponding entry in the analysisfeature table. analysisfeatures will have two or more featureloc entries, with rank indicating query/subject
| F-Key | Name | Type | Description |
|---|---|---|---|
| analysisfeature_id | serial | PRIMARY KEY | |
| feature_id | integer | UNIQUE#1 NOT NULL | |
| analysis_id | integer | UNIQUE#1 NOT NULL | |
| rawscore | double precision | 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. | |
| normscore | double precision | 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. | |
| significance | double precision | 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. | |
| identity | double precision | 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. |
Table: analysisprop
| F-Key | Name | Type | Description |
|---|---|---|---|
| analysisprop_id | serial | PRIMARY KEY | |
| analysis_id | integer | UNIQUE#1 NOT NULL | |
| type_id | integer | UNIQUE#1 NOT NULL | |
| value | text | UNIQUE#1 |
