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A | B | C | D | E | F | G | H | |
1 | Serial Number | Table name | Table definition | Field name | Field definition | Source | Field type | Details |
2 | 1 | Sequence sample(SSAM) | Information about sample from which sequence originated | SE id(SSAM) | Integer sequence ID | DB-generated | Int | |
3 | PAT id(SSAM) | Integer patient ID | DB-generated | Int | ||||
4 | Name | Sequence name | Curation or GB record | Text | ||||
5 | Locus name | Locus name | GB record | Text | ||||
6 | Isolate name | Isolate name | GB record | Text | ||||
7 | Clone name | Clone name | GB record | Text | ||||
8 | Georegion | Geographical region of sample origin | Generated from Country | CV | Africa, Sub-Saharan Africa, Antarctica, Asia, Caribbean, Central America, Europe, Former USSR, Middle East, North America, Oceania, South America |
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9 | Country | Sampling country | Curation or GB record | CV | ISO 2-letter country codes | |||
10 | Sampling city | Sampling city or region | Curation or GB record | Text | ||||
11 | Sampling year | Sampling date (only month and year will be displayed) | Curation or GB record | date | ||||
12 | Sampling year upper | Sampling year upper bound if range | Curation or GB record | date | ||||
13 | Patient Age | Patient age in days at time of sampling | Curation | Int | ||||
14 | Patient health | Health status at time of sampling | Curation | CV | acute infection, asymptomatic, symptomatic, AIDS, deceased |
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15 | Organism | Virus species | GB record | CV | HIV-1, HIV-2, SIV, SHIV, synthetic DNA |
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16 | Subtype | Subtype clade of virus | Curation or GB record | CV | ||||
17 | Phenotype | Syncytium inducing phenotype | Curation | CV | SI, NSI |
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18 | Coreceptor | Co-receptor(s) used | Curation | Text | Space separated list of co-receptors | |||
19 | Sample tissue | Sample tissue ("body part") from which virus was derived | Curation or GB record | CV | List available in Main Search Interface (under "More sequence information") | |||
20 | Culture method | Was virus cultured before isolation? | Curation | CV | Cultured, Expanded, Primary, Uncultured |
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21 | Molecule type | Where the virus was isolated from | Curation or GB record | CV | DNA, RNA |
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22 | Drug naive | Was patient treated before sample was taken? | Curation | boolean | Yes, No |
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23 | Problematic | Is there a problem with the sequence? | Curation or DB-generated | Int / CV | N: Non-ACTG characters, C: Contaminant, H: Hypermutant, S: Synthetic, D: Deletion, T: Tiny, R: Reverse complement |
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24 | Viral load | HIV viral load at time of sample | Curation | Int | ||||
25 | CD4 count | CD4 count at time of sample | Curation | Int | ||||
26 | CD8 count | CD8 count at time of sample | Curation | Int | ||||
27 | Days from infection | Number of days between time of infection and time sample was taken |
Curation | Int | ||||
28 | Days from seroconversion | Number of days between patient’s seroconversion and day sample was taken | Curation | Int | ||||
29 | Days from first sample | Number of days between first sample and current sample | Curation | Int | ||||
30 | Sequencing method | Denotes if the sample was cloned or sequenced directly | Curation | CV | Clone, Direct |
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31 | Amplification strategy | Denotes how the sample was amplified before sequencing | Curation | CV | bulk, SGA, limiting dilution PCR |
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32 | Fiebig stage | The stage of early HIV infection | Curation | CV | Stages described in Search Help | |||
33 | Annotated | Denotes if the record has ever been manually curated | Curation | boolean | True, false | |||
34 | Days from treatment start | Number of days between treatment start and sample date | Curation | Int | ||||
35 | Days from treatment end | Number of days between treatment end and sample date | Curation | Int | ||||
36 | 2 | Patient(PAT) | Information about patient | PAT id | Integer patient ID | DB-generated | Int | |
37 | Patient code | Code or name for patient in publication | Curation | Text | ||||
38 | Patient sex | Patient sex | Curation | CV | M or F | |||
39 | Risk factor | probable route of infection | Curation | CV | SB: bisexual, PB: blood transfusion, EX: experimental, PH: hemophiliac, SH: heterosexual, SW: sex worker, SG: homosexual, SU: sexual undescribed, PI: IV drug user, SM: male sex with male, MB: mother-baby, NO: nosocomial, OT: other, NR: not recorded |
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40 | Infection country | Infection country if different from sampling country | Curation | CV | ISO 2-letter country codes | |||
41 | Infection city | Infection city or region if different from sampling city or region | Curation | Text | ||||
42 | Infection year | Infection date (only month and year displayed) | Curation | date | ||||
43 | Patient comment | Comments about patient | Curation | Text | ||||
44 | HLA type | Any information about the patient's HLA types | Curation | Text | ||||
45 | Project | Project or cohort enrolled by patient | Curation | CV | List available in Main Search Interface (under "Patient information") | |||
46 | Patient ethnicity | Ethnicity of patient | Curation | CV | ||||
47 | Progression | Rate of progression of the patient | Curation | CV | EC: elite controller, LTNP: long-term non-progressor, SP: slow progressor, RP: rapid progressor, P: progressor |
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48 | # of patient seqs | # of sequences linked to patient | DB-generated | Int | To find patients who have more than N sequences | |||
49 | # of patient timepoints | # timepoints available from this patient | DB-generated | Int | To find patients with longitudinal data | |||
50 | Host species | SIV host species | Curation | Text | ||||
51 | 3 | Accession(SA) | SE id(SA) | Integer sequence ID | DB-generated | Int | ||
52 | Accession | GenBank Accession | GB record | Text | ||||
53 | GI number | GI number | GB record | Int | ||||
54 | Version | Version name | GB record | Text | ||||
55 | 4 | Map Image(MI) | Information about sequence co-ordinates | Map image(SE id) | Integer sequence ID | DB-generated | Int | These coordinates are the HXB2 or Mac239 coordinates. |
56 | MI start | start position | Imported | Int | ||||
57 | MI stop | stop position | Imported | Int | ||||
58 | 5 | Sequence Map(SM) | Information about sequence co-ordinates | SE id(SM) | Integer sequence ID | DB-generated | Int | System of internal database coordinates; the SM fields are not included in the Advanced Search |
59 | SM start | start position | Imported | Int | ||||
60 | SM stop | stop position | Imported | Int | ||||
61 | 6 | Sequence Entry(SE) | Information about a sequence obtained from GenBank | SE id | Integer sequence ID | DB-generated | Int | |
62 | Sequence length | Number of nucleotides | GB record | Int | ||||
63 | GB comment | Comment from GB | GB record | Text | ||||
64 | DB comment | Comment from HIV DB staff | Curation | Text | ||||
65 | Sequence | Actual sequence | GB record | Text | ||||
66 | GB create date | GB create date | GB record | date | ||||
67 | GB update date | GB update date | GB record | date | ||||
68 | 7 | Publication Links(SPL) | Information to link publication and sequence | SE id(SPL) | Integer sequence ID | DB-generated | Int | |
69 | PUB id(SPL) | Integer publication ID | DB-generated | Int | ||||
70 | Publication number | Publication number | DB-generated | Int | ||||
71 | 8 | Publication(PUB) | Information about publication that describes sequence | PUB id(SPL) | Integer publication ID | DB-generated | Int | |
72 | Pubmed ID | Pubmed ID of a published paper | Curation or GB record | Int | ||||
73 | Title | Title of the publication | GB record | Text | ||||
74 | Journal | Journal name | GB record | Text | ||||
75 | Consortium | Consortium name | GB record | Text | ||||
76 | 9 | Person(PER) | Information about authors listed on publication | PER id | Integer person ID | DB-generated | Int | |
77 | Last name | Last name of the author | GB record | Text | ||||
78 | 10 | Author(AU) | Information to link publication and author | PUB id(AU) | Integer publication ID | DB-generated | Int | |
79 | PER id(AU) | Integer person ID | DB-generated | Int | ||||
80 | Author number | Author number | DB-generated | Int | ||||
81 | 11 | Sequence Entry Feature(SEF) | Information about a sequence entry feature | SE id(SEF) | Integer sequence ID | DB-generated | Int | |
82 | Feature type(SEF) | Sequence entry feature type | GB record | CV | ||||
83 | Description(SEF) | Sequence entry feature description | GB record | Text | ||||
84 | PUB id(SEF) | Integer publication ID | DB-generated | Int | ||||
85 | 12 | Location(LOC) | Information about a feature that has a location in the sequence | LOC id | Integer location ID | DB-generated | Int | |
86 | SE id(LOC) | Integer sequence ID | DB-generated | Int | ||||
87 | Feature type(LOC) | Location feature type | GB record | CV | ||||
88 | Description(LOC) | Location description | GB record | Text | ||||
89 | 13 | Sequence Feature(SF) | Information about a sequence feature | LOC id(SF) | Integer location ID | DB-generated | Int | |
90 | Feature type(SF) | Sequence feature type | GB record | CV | ||||
91 | Feature value(SF) | Sequence feature value | GB record | Text | ||||
92 | 14 | Cluster(CLU) | Information about a cluster, which is a group of patients epidemiologically linked | CLU id(CLU) | Integer cluster ID | DB-generated | Int | |
93 | Cluster name | Name assigned to each linked cluster of patients | Curation | Text | List available in Main Search Interface (under "Patient information", "More patient information") | |||
94 | Cluster description | Comments describing cluster | Curation | Text | ||||
95 | PUB id(CLU) | Integer publication ID associated with cluster | DB-generated | Int | ||||
96 | 15 | Cluster Link(CPL) | Information to link cluster to patients | CLU id(CPL) | Integer cluster ID | DB-generated | Int | |
97 | PAT id(CPL) | Integer patient ID | DB-generated | Int | ||||
98 | Cluster transmission type | Mode(s) of viral transmission among patients in cluster | Curation | Text | SB: bisexual, PB: blood transfusion, EX: experimental, PH: hemophiliac, SH: heterosexual, SG: homosexual, SU: sexual undescribed, PI: IV drug user, SM: male sex with male, MB: mother-baby, NO: nosocomial, OT: other, NR: not recorded |