转自：http://www.biotrainee.com/thread-411-1-1.html
常用数据库 ID
| ID 示例 | ID 来源 |
| ENSG00000116717 | Ensemble ID |
| GA45A_HUMAN | UniProtKB/Swiss-Prot, entry name |
| A5PJB2_BOVIN | UniProtKB/TrEMBL, entry name |
| A2BC19, P12345, A0A022YWF9 | UniProt, accession number |
| GLA, GLB, UGT1A1 | HGNC Gene Symbol |
| U12345, AF123456 | GenBank, NCBI, accession number |
| NT_123456, NM_123456, NP_123456 | RefSeq, NCBI, accession number |
| 10598, 717 | Entrez ID, NCBI |
| uc001ett, uc031tla.1 | UCSC ID |
Ensembl stable IDs
Ensembl stable ID 的结构是根据不同物种设置的前缀, 加上数据所指的类型, 如基因蛋白质, 再加上一系列的数字. 有的时候可以有不同的版本, 则在 Ensembl ID 后面加上小数点和版本号.
常用物种前缀
| 前缀 | 学名 |
| ENSCEL | Caenorhabditis elegans (Caenorhabditis elegans) |
| ENSCAF | Canis lupus familiaris (Dog) |
| ENSDAR | Danio rerio (Zebrafish) |
| FB | Drosophila melanogaster (Fruitfly) |
| ENS | Homo sapiens (Human) |
| ENSMUS | Mus musculus (Mouse) |
| ENSRNO | Rattus norvegicus (Rat) |
| ENSXET | Xenopus tropicalis (Xenopus) |
类型前缀
| 前缀 | 类型 |
| E | exon |
| FM | Ensembl protein family |
| G | gene |
| GT | gene tree |
| P | protein |
| R | regulatory feature |
| T | transcript |
UniProt
UniProt 中录入的数据都被分配了一个唯一的 entry name.
UniProtKB/Swiss-Prot entry name
UniProtKB/Swiss-Prot entry name 是最多有 11 位包含大写字母的字符串, 一般有着 "X_Y" 的形式, 其中 "X" 是最多五个便于记忆的蛋白质编号, "_" 是下划线, "Y" 是最多五个便于记忆的物种编号.
蛋白质编号示例如下:
| Code(X) | Recommended protein name | Gene name |
| B2MG | Beta-2-microglobulin | B2M |
| HBA | Hemoglobin subunit alpha | HBA1 |
| INS | Insulin | INS |
| CAD17 | Cadherin-17 | CDH17 |
物种编号示例如下:
| Code | Species |
| BOVIN | Bovine |
| CHICK | Chicken |
| ECOLI | Escherichia coli |
| HORSE | Horse |
| HUMAN | Homo sapiens |
| MAIZE | Maize (Zea mays) |
| MOUSE | Mouse |
| PEA | Garden pea (Pisum sativum) |
| PIG | Pig |
| RABIT | Rabbit |
| RAT | Rat |
| SHEEP | Sheep |
| SOYBN | Soybean (Glycine max) |
| TOBAC | Common tobacco (Nicotina tabacum) |
| WHEAT | Wheat (Triticum aestivum) |
| YEAST | Baker’s yeast (Saccharomyces cerevisiae) |
UniProtKB/TrEMBL entry name
UniProtKB/TrEMBL entry name 是最多 16 位包含大写字母的字符串, 一般有着 "X_Y" 的形式, 其中 "X" 是
6 到 10 个字符组成的 accession number, "_" 是下划线, "Y" 是最多五个便于记忆的物种编号.
Accession Number
UniProtKB 的 Accession Number 相当于数据库的主键, 由 6 到 10 个大写字母或者数字组成. 其构成规律为:
[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}
实际上, accession number 是三种类型:
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| [O P Q] | [0-9] | [A-Z 0-9] | [A-Z 0-9] | [A-Z 0-9] | [0-9] | ||||
| [A-N R-Z] | [0-9] | [A-Z] | [A-Z 0-9] | [A-Z 0-9] | [0-9] | ||||
| [A-N R-Z] | [0-9] | [A-Z] | [A-Z 0-9] | [A-Z 0-9] | [0-9] | [A-Z] | [A-Z 0-9] | [A-Z 0-9] | [0-9] |
如果一个条目被分成两个, 或者多个条目合成一个, 则有相应的 accession number 继承规则.
HUGO Gene Nomenclature Committee
Gene Symbol
Gene Symbol 是用来表示基因的编码, 由大写字母构成, 或由大写字母和数字构成, 首字母均应该是字母.
如: GLA "galactosidase, alpha"; GLB "galactosidase, beta"; UGT1A1 "UDP
glycosyltransferase 1 family, polypeptide A1" 再到 UGT1A13 代表了 13 个不同的
gene symbol.
NCBI
GenBank Accession Number
GenBank 的通用 accession number 通常是由一个大写字母加上 5 个数字的组合, 或者两个大写字母加上 6 个数字的组合.
RefSeq Accession Number
RefSeq 有一套特殊的 Accesion Number. 形式是: [A-Z]{2}[_][0-9]{6:}, 两个大写字母, 一个下划线, 6 个或更多的数字.
| Accession 前缀 | 类型 | 说明 |
| AC_ | Genomic | Complete genomic molecule, usually alternate assembly |
| NC_ | Genomic | Complete genomic molecule, usually reference assembly |
| NG_ | Genomic | Incomplete genomic region |
| NT_ | Genomic | Contig or scaffold, clone-based or WGS |
| NW_ | Genomic | Contig or scaffold, primarily WGS |
| NS_ | Genomic | Environmental sequence |
| NZ_ | Genomic | Unfinished WGS |
| NM_ | mRNA | |
| NR_ | RNA | |
| XM_ | mRNA | Predicted model |
| XR_ | RNA | Predicted model |
| AP_ | Protein | Annotated on AC_ alternate assembly |
| NP_ | Protein | Associated with an NM_ or NC_ accession |
| YP_ | Protein | |
| XP_ | Protein | Predicted model, associated with an XM_ accession |
| ZP_ | Protein | Predicted model, annotated on NZ_ genomic records |
- WGS: Whole Genome Shotgun sequence data, 鸟枪法测序.
Entrez ID
Entrez 是 NCBI 使用的能够对众多数据库进行联合搜索的搜索引擎, 其对不同的 Gene 进行了编号, 每个 gene 的编号就是
entrez gene id. 由于 entrez id 相对稳定, 所以也被众多其他数据库, 如 KEGG 等采用. Entrez Gene
ID 就是一系列数字, 也比较容易辨识. R 或网站都有众多的工具可以帮助从不同的 ID 转换为 entrez id 或者反向转换.
UCSC ID
UCSC ID 由小写字母和数字构成, 起始均为 uc, 然后是三位数字, 接着又是三位小写字母, 最后有小数点和数字构成版本号.
如: uc010qfk.3, uc010qfk.3.
