| Column | MySQL Type | Oracle Type | Nullable | Description |
|---|---|---|---|---|
| WID | BIGINT | NUMBER | No | Warehouse identifier for this NucleicAcid. |
| Name | VARCHAR | VARCHAR2(200) | Yes | Name or description of this molecule. Ex: (CMR) 'Chromosome II Brucella melitensis 16M'. |
| Type | VARCHAR | VARCHAR2(30) | No | Enumeration: 'DNA' 'RNA' or 'na' Enumerated Values:
DNA - The molecule is composed of DNA RNA - The molecule is composed of RNA NA - The molecule is specified as a nucleic acid but whether of type DNA or RNA is not known |
| Class | VARCHAR | VARCHAR2(30) | Yes | Enumeration: describes the molecule as it exists in the organism; stores values such as RNA subtype
("pre-RNA", "mRNA"), replicon type (e.g., "chromosome", "plasmid")
Enumerated Values:
pre-RNA - As it exists within the organism, the molecule is a pre-RNA molecule. NCBI: used when there is no evidence that mature RNA is produced mRNA - As it exists within the organism, the molecule is a mature mRNA. NCBI: used when there is evidence that mature mRNA is produced rRNA - As it exists within the organism, the molecule is an rRNA; NCBI used when there is evidence that mature rRNA is produced tRNA - As it exists within the organism, the molecule is a tRNA; NCBI: used when there is evidence that mature tRNA is produced snRNA - As it exists within the organism, the molecule is a small nuclear RNA. NCBI: used when there is evidence that snRNA is produced scRNA - As it exists within the organism, the molecule is an RNA which encodes small cytoplasmic ribonucleic proteins. NCBI: used when there is evidence that gene codes of small cytoplasmic (sc) ribonucleoproteins (RNP)s snoRNA - As it exists within the organism, the molecule is a small nucleolar RNA. NCBI: used when there is evidence that transcript is a small nucleolar RNA other - Check notes as to how we map this... chromosome - As it exists within the organism, the molecule is a chromosome plasmid - As it exists within the organism, the molecule is a plasmid organelle-chromosome - As it exists within the organism, the molecule is the chromosome of an organelle transposon - As it exists within the organism, the molecule is a transposon virus - As it exists within the organism, the molecule is a virus unknown - Used when the class is unknown |
| Topology | VARCHAR | VARCHAR2(30) | Yes | Enumeration: 'circular', 'linear' or 'other'. Enumerated Values:
linear - The topology of the molecule is Linear circular - The topology of the molecule is Circular other - The topology of the molecule is neither circular nor linear but is known |
| Strandedness | VARCHAR | VARCHAR2(30) | Yes | Enumeration indicating whether Nucleic Acid is single stranded, double stranded or mixed
stranded.
Enumerated Values:
ss - The molecule is single stranded ds - The molecule is double stranded mixed - The molecule is composed of single and double stranded regions |
| SequenceDerivation | VARCHAR | VARCHAR2(30) | Yes | Enumeration describing how the sequence was generated (e.g., from single clone, from assembly of sequences from other sequence entries, collection of different clones, etc). Enumerated Values:
virtual - NCBI: The sequence of the molecule is NOT known. NOTE: this should map to null. raw - POORLY DEFINED; seems to be used to indicate that the sequence of the molecule was actually generated from one single continuous molecule, as opposed to assembled together from sequences from different molecules (e.g., different clones) seg - NCBI: The sequence of the molecule is made up of collection of segments arranged according to specified coordinates, e.g., sequence was derived from assembling sequences from different clones reference - NCBI: The sequence of the molecule is constructed from existing Bioseqs;It behaves exactly like a segmented Bioseq in taking it's data and character from the Bioseq to which it points. constructed - NCBI: The sequence of the molecule is constructed by assembling other Bioseqs consensus - NCBI: The sequence of the molecule represents a pattern typical of a sequence region or family of sequences;' it summarizes attributes of an aligned collection of real sequences. Note that this is NOT A REAL OBJECT map - NCBI: The molecule does not have a sequence describing it, but rather a set of coordinates (restriction fragment order, genetic markers, physical map, etc) |
| Fragment | CHAR(1) | CHAR(1) | Yes | 'T' if this is a fragment of a molecule, 'F' if this NucleicAcid describes an entire molecule. |
| FullySequenced | CHAR(1) | CHAR(1) | Yes | 'T' if the molecule is completely sequenced within this dataset, else 'F'. |
| MoleculeLength | INT | NUMBER | Yes | The length of the molecule, in nucleotides. This value is firm if FullySequenced is 'T'; otherwise,MoleculeLength is an approximation and is not necessarily equal to CumulativeLength, as the the molecule may not have been sequenced to completion. This value is calculated if it is not explicitely stated in the source dataset |
| MoleculeLengthApproximate | VARCHAR | VARCHAR2(10) | Yes | Enumeration; specifies whether MoleculeLength stores an approximate value: 'gt' for greater than, 'lt' for less than, or 'ne' for not equal. Enumerated Values:
gt - The length of the molecule's sequence is greater than the actual length specified lt - The length of the molecule's sequence is less than the actual length specified ne - The length of the molecule's sequence is less than or greater than the actual length. All we know is that its not the exact length |
| CumulativeLength | INT | NUMBER | Yes | The cumulative number of nucleotides for all Subsequences referenced by this NucleicAcid
entry,
whether contiguous or not. This value is a summation of the number of nucleotides for these Subsequences. If the molecule is completely sequenced, this value should be identical to that of MoleculeLength, and both fields are populated. |
| CumulativeLengthApproximate | VARCHAR | VARCHAR2(10) | Yes | Enumeration; specifies whether CumulativeLength how approximates actual total length: 'gt' for greater than, 'lt' for less than, or 'ne' for not equal. Enumerated Values:
gt - The total length of the molecule's sequence is greater than the actual length lt - The total length of the molecule's sequence is less than the actual length ne - The total length of the molecule's sequence is less than or greater than the actual length. All we know is that its not the exact length |
| GeneticCodeWID | BIGINT | NUMBER | Yes | References the genetic code of this molecule. |
| BioSourceWID | BIGINT | NUMBER | Yes | References the biological source of this molecule. |
| DataSetWID | BIGINT | NUMBER | No | References the data set from which the entity came from |
| Table | Column |
|---|---|
| Subsequence | NucleicAcidWID |
| Gene | NucleicAcidWID |
| GeneWIDNucleicAcidWID | NucleicAcidWID |
| Entry | OtherWID |
| Support | OtherWID |
| InteractionParticipant | OtherWID |
| RelatedTerm | OtherWID |
| CitationWIDOtherWID | OtherWID |
| CommentTable | OtherWID |
| CrossReference | OtherWID |
| CrossReference | CrossWID |
| Description | OtherWID |
| DBID | OtherWID |
| SynonymTable | OtherWID |
| ToolAdvice | OtherWID |
| Name | Columns |
|---|---|
| NUCLEICACID_Name | Name |
| NUCLEICACID_Type | Type |
| NUCLEICACID_Class | Class |
| NUCLEICACID_MoleculeLength | MoleculeLength |
| NUCLEICACID_CumulativeLength | CumulativeLength |
| NUCLEICACID_GCWID | GeneticCodeWID |
| NUCLEICACID_BSWID | BioSourceWID |
| NUCLEICACID_DATASETWID | DATASETWID |