| Column | MySQL Type | Oracle Type | Nullable | Description |
|---|---|---|---|---|
| WID | BIGINT | NUMBER | No | Warehouse identifier of this feature. |
| Description | VARCHAR | VARCHAR2(1300) | Yes | Textual description of this feature. |
| Type | VARCHAR | VARCHAR2(50) | Yes | Type of feature. These type values come from the source dataset and are not necessarily enumerated. Example: "Promoter CYZ". |
| Class | VARCHAR | VARCHAR2(50) | Yes | Class of feature. Assigns our typology for types of features, or qualifiers associated with features. These are our own enumerated type values, to allow us to classify features without losing the original (author-provided) type values stored in Type. Example: Class=promoter. Enumerated Values:
binding site - Identifies the presence of a DNA binding site promoter - Identifies the presence of a promoter terminator - Identifies the presence of a terminator pseudogene - Identifies a pseudogene, whether non-transcribed or processed ORF - Identifies a truly unknown open reading frame according to warehouse definition (no strong evidence that a product is produced) partial - Qualifier: States that feature is not complete unknown product - Identifies an unspecified product is produced from this genomic location, as stated in dataset notable - Qualifier: Characterizes the feature value as notable (same as 'Exceptional' in GB dataset) by similarity - Qualifier: states that feature was derived by similarity analysis potential - Qualifier: states that feature may be incorrect probably - Qualifier: states that feature is probably correct |
| SequenceType | CHAR(1) | CHAR(1) | No | Enumeration (see also SequenceWID) that indicates whether the sequence is protein or nucleic and how the sequence (if available) is represented: If 'P', feature resides on a protein. If 'S' or 'N', feature resides on a nucleic acid. Enumerated Values:
P - Feature resides on a protein. Implies SequenceWID (if nonNULL) references a Protein S - Feature resides on a nucleic acid. Implies SequenceWID is nonNULL and references a Subsequence N - Feature resides on a nucleic acid. Implies SequenceWID (if nonNULL) references a NucleicAcid |
| SequenceWID | BIGINT | NUMBER | Yes | References the Protein or Subsequence containing the sequence on which we are defining a feature: SequenceType of 'S' implies SequenceWID is nonNULL and references a Subsequence- sequence = Subsequence.Sequence (i.e., it is stored explicitly), SequenceType of 'N' implies SequenceWID (if nonNULL) references a NucleicAcid- sequence is the substring Subsequence.Sequence[StartPosition : EndPosition] where Subsequence is the full Subsequence of the nucleic acid. SequenceType of 'P' implies SequenceWID (if nonNULL) references a Protein- sequence is the substring Protein.AASequence[StartPosition : EndPosition]. |
| Variant | LONGTEXT | CLOB | Yes | Amino-acid sequence for this protein, if available |
| RegionOrPoint | VARCHAR | VARCHAR2(10) | Yes | Specifies whether this feature is specified with starting and ending coordinates or with a single coordinate. Enumerated Values:
region - Feature is specified by a start point and an end point on the sequence point - Feature is specified by a single point on the sequence |
| PointType | VARCHAR | VARCHAR2(10) | Yes | Only defined if RegionOrPoint='point'. Specifies where the feature is relative to its location as encoded in StartPosition and EndPosition: Enumerated Values:
center - Feature is centered at location. left - Feature extends to the left (decreasing position) of location. right - Feature extends to the right (increasing position) of location. |
| StartPosition | INT | NUMBER | Yes | Start position of the feature within the NucleicAcid or Protein sequence. If Feature.RegionOrPoint is 'point', StartPosition and EndPosition will either be equal (location is exactly at a nucleotide or amino acid) or will differ by 1 (location is centered between two adjacent nucleotides or amino acids). |
| EndPosition | INT | NUMBER | Yes | End position of the feature within the NucleicAcid or Protein sequence. If Feature.RegionOrPoint is 'point', StartPosition and EndPosition will either be equal (location is exactly at a nucleotide or amino acid) or will differ by 1 (location is between two adjacent nucleotides or amino acids). |
| StartPositionApproximate | VARCHAR | VARCHAR2(10) | Yes | Indicates that the Start position of the coding region is an approximate value It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not equal. This is a controlled vocabulary. Enumerated Values:
gt - The start position of the feature is greater than the actual position specified. lt - The start position of the feature is less than the actual position specified. ne - The start position of the feature is less than or greater than the actual position. All we know is that its not the exact position. |
| EndPositionApproximate | VARCHAR | VARCHAR2(10) | Yes | Indicates that the End position of the coding region is an approximate value. It could be 'gt' for greater than, 'lt' for less than and 'ne' to indicate that it is not equal. This is a controlled vocabulary. Enumerated Values:
gt - The end position of the feature is greater than the actual position specified. lt - The end position of the feature is less than the actual position specified. ne - The end position of the feature is less than or greater than the actual position. All we know is that its not the exact position. |
| ExperimentalSupport | CHAR(1) | CHAR(1) | Yes | 'T' if the feature is supported by experimental evidence, else 'F' |
| ComputationalSupport | CHAR(1) | CHAR(1) | Yes | 'T' if the feature is supported by computational evidence, else 'F' |
| DataSetWID | BIGINT | NUMBER | No | Reference to the data set from which the entity came from |
| Column | References |
|---|---|
| SequenceWID | Subsequence : WID |
| SequenceWID | Protein : WID |
| Table | Column |
|---|---|
| SeqFeatureLocation | SeqFeature_Regions |
| Entry | OtherWID |
| TranscriptionUnitComponent | OtherWID |
| Support | OtherWID |
| RelatedTerm | OtherWID |
| CitationWIDOtherWID | OtherWID |
| CommentTable | OtherWID |
| CrossReference | OtherWID |
| CrossReference | CrossWID |
| Description | OtherWID |
| DBID | OtherWID |
| SynonymTable | OtherWID |
| ToolAdvice | OtherWID |
| Name | Columns |
|---|---|
| FEATURE_Description | |
| FEATURE_TYPE | Type |
| FEATURE_Class | Class |
| FEATURE_SequenceWID | SequenceWID |
| FEATURE_START_ENDPOS | STARTPOSITION,ENDPOSITION |
| FEATURE_ENDPOSITION | ENDPOSITION |
| FEATURE_DATASETWID | DATASETWID |