# Description of Schema

## Tables

analysis
analysisprop
analysisfeature
analysisfeatureprop
analysis_dbxref
analysis_cvterm
analysis_relationship
analysis_pub

### analysis

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Comments:
$Id: companalysis.sql,v 1.37 2007-03-23 15:18:02 scottcain Exp $
==========================================
Chado companalysis module
=================================================================
Dependencies:
:import feature from sequence
:import cvterm from cv
:import dbxref from db
:import pub from pub
=================================================================
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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.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysis_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
name | varchar | 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 | 64000 |  |  |
program | varchar | 255 |  | UNIQUE, NOT NULL, Program name, e.g. blastx, blastp, sim4, genscan. |
programversion | varchar | 255 |  | UNIQUE, NOT NULL, Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000]. |
algorithm | varchar | 255 |  | Algorithm name, e.g. blast. |
sourcename | varchar | 255 |  | UNIQUE, Source name, e.g. cDNA, SwissProt. |
sourceversion | varchar | 255 |  |  |
sourceuri | text | 64000 |  | 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 | 0 | current_timestamp | NOT NULL |

### Constraints

Type | Fields
--- | ---
NOT NULL | analysis_id
NOT NULL | program
NOT NULL | programversion
NOT NULL | timeexecuted
UNIQUE | program, programversion, sourcename

### analysisprop

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Comments:
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TABLE: analysisprop
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Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysisprop_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
analysis_id | integer | 20 |  | UNIQUE, NOT NULL | analysis.analysis_id
type_id | integer | 20 |  | UNIQUE, NOT NULL | cvterm.cvterm_id
value | text | 64000 |  |  |
rank | integer | 10 | 0 | UNIQUE, NOT NULL |

### Indices

Name | Fields
--- | ---
analysisprop_idx1 | analysis_id
analysisprop_idx2 | type_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysisprop_id
NOT NULL | analysis_id
FOREIGN KEY | analysis_id
NOT NULL | type_id
FOREIGN KEY | type_id
NOT NULL | rank
UNIQUE | analysis_id, type_id, rank

### analysisfeature

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Comments:
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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

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysisfeature_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
feature_id | integer | 20 |  | UNIQUE, NOT NULL | feature.feature_id
analysis_id | integer | 20 |  | UNIQUE, NOT NULL | analysis.analysis_id
rawscore | float | 20 |  | 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

float

20

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

float

20

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 | float | 20 |  | 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. |

### Indices

Name | Fields
--- | ---
analysisfeature_idx1 | feature_id
analysisfeature_idx2 | analysis_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysisfeature_id
NOT NULL | feature_id
FOREIGN KEY | feature_id
NOT NULL | analysis_id
FOREIGN KEY | analysis_id
UNIQUE | feature_id, analysis_id

### analysisfeatureprop

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Comments:
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TABLE: analysisfeatureprop
================================================

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysisfeatureprop_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
analysisfeature_id | integer | 20 |  | UNIQUE, NOT NULL | analysisfeature.analysisfeature_id
type_id | integer | 20 |  | UNIQUE, NOT NULL | cvterm.cvterm_id
value | text | 64000 |  |  |
rank | integer | 10 |  | UNIQUE, NOT NULL |

### Indices

Name | Fields
--- | ---
analysisfeatureprop_idx1 | analysisfeature_id
analysisfeatureprop_idx2 | type_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysisfeature_id
FOREIGN KEY | analysisfeature_id
NOT NULL | type_id
FOREIGN KEY | type_id
NOT NULL | rank
UNIQUE | analysisfeature_id, type_id, rank
FOREIGN KEY | analysisfeature_id
FOREIGN KEY | type_id

### analysis_dbxref

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Comments:
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TABLE: analysis_dbxref
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Links an analysis to dbxrefs.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysis_dbxref_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
analysis_id | integer | 20 |  | UNIQUE, NOT NULL | analysis.analysis_id
dbxref_id | integer | 20 |  | UNIQUE, NOT NULL | dbxref.dbxref_id
is_current | boolean | 0 | true | NOT NULL, True if this dbxref is the most up to date accession in the corresponding db. Retired accessions should set this field to false |

### Indices

Name | Fields
--- | ---
analysis_dbxref_idx1 | analysis_id
analysis_dbxref_idx2 | dbxref_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysis_dbxref_id
NOT NULL | analysis_id
NOT NULL | dbxref_id
NOT NULL | is_current
FOREIGN KEY | analysis_id
FOREIGN KEY | dbxref_id
UNIQUE | analysis_id, dbxref_id

### analysis_cvterm

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Comments:
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TABLE: analysis_cvterm
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Associate a term from a cv with an analysis.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysis_cvterm_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
analysis_id | integer | 20 |  | UNIQUE, NOT NULL | analysis.analysis_id
cvterm_id | integer | 20 |  | UNIQUE, NOT NULL | cvterm.cvterm_id
is_not | boolean | 0 | false | NOT NULL, 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. |
rank | integer | 10 | 0 | UNIQUE, NOT NULL |

### Indices

Name | Fields
--- | ---
analysis_cvterm_idx1 | analysis_id
analysis_cvterm_idx2 | cvterm_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysis_cvterm_id
NOT NULL | analysis_id
NOT NULL | cvterm_id
NOT NULL | is_not
NOT NULL | rank
FOREIGN KEY | analysis_id
FOREIGN KEY | cvterm_id
UNIQUE | analysis_id, cvterm_id, rank

### analysis_relationship

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Comments:
================================================
TABLE: analysis_relationship
================================================

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysis_relationship_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
subject_id | integer | 20 |  | UNIQUE, NOT NULL, analysis_relationship.subject_id i s the subject of the subj-predicate-obj sentence. | analysis.analysis_id
object_id | integer | 20 |  | UNIQUE, NOT NULL, analysis_relationship.object_id is the object of the subj-predicate-obj sentence. | analysis.analysis_id
type_id | integer | 20 |  | UNIQUE, NOT 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. | cvterm.cvterm_id
value | text | 64000 | NULL | analysis_relationship.value is for additional notes or comments. |
rank | integer | 10 | 0 | UNIQUE, NOT NULL, 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. |

### Indices

Name | Fields
--- | ---
analysis_relationship_idx1 | subject_id
analysis_relationship_idx2 | object_id
analysis_relationship_idx3 | type_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysis_relationship_id
NOT NULL | subject_id
NOT NULL | object_id
NOT NULL | type_id
NOT NULL | rank
FOREIGN KEY | subject_id
FOREIGN KEY | object_id
FOREIGN KEY | type_id
UNIQUE | subject_id, object_id, type_id, rank

### analysis_pub

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Comments:
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TABLE: analysis_pub
================================================
Provenance. Linking table between analyses and the publications that mention them.

Field Name | Data Type | Size | Default Value | Other | Foreign Key
--- | --- | --- | --- | --- | ---
analysis_pub_id | integer | 20 |  | PRIMARY KEY, NOT NULL |
analysis_id | integer | 20 |  | UNIQUE, NOT NULL | analysis.analysis_id
pub_id | integer | 20 |  | UNIQUE, NOT NULL | pub.pub_id

### Indices

Name | Fields
--- | ---
analysis_pub_idx1 | analysis_id
analysis_pub_idx2 | pub_id

### Constraints

Type | Fields
--- | ---
NOT NULL | analysis_pub_id
NOT NULL | analysis_id
FOREIGN KEY | analysis_id
NOT NULL | pub_id
FOREIGN KEY | pub_id
UNIQUE | analysis_id, pub_id

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