ChEMBL

实用信息

内容范围

• 该页面称 ChEMBL 是一个生物活性类药小分子数据库，包含二维结构、计算属性（如 logP、分子量）以及抽取的生物活性数据。
  chembl.gitbook.io · 2026-11-13

  ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).

  https://chembl.gitbook.io/chembl-interface-documentation/about · 数据集页面 · 核实于 2026-11-13

• 文本说明这些数据从原始科学文献中抽取和整理，覆盖现代药物构效关系（SAR）与发现的相当一部分。
  chembl.gitbook.io · 2026-11-13

  The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs

  https://chembl.gitbook.io/chembl-interface-documentation/about · 数据集页面 · 核实于 2026-11-13

标识符

• ChEMBL_ID文本说明子结构与相似性服务接受 SMILES、InChI Key 和分子 ChEMBL_ID 作为参数。
  chembl.gitbook.io · 2026-11-13

  These methods accept SMILES, InChI Key and molecule ChEMBL_ID as arguments and in the case of similarity searches an additional identity cut-off is needed.

  https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services · 数据集页面 · 核实于 2026-11-13

• → 其他资源（未写明）X-Ref 端点被描述为提供化合物与其他资源之间的交叉引用。
  chembl.gitbook.io · 2026-11-13

  Cross references to other resources for compounds

  https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services · 数据集页面 · 核实于 2026-11-13

取用方式

• 批量下载ftp.ebi.ac.uk SDF · FASTA · MySQL · PostgreSQL · SQLite · FP · H5 · XML · TXT · PNG
  • 单独条款：商用 未写明 · 再分发 有条件
    ftp.ebi.ac.uk · 2026-11-13

    The data content in ChEMBL is licensed under a highly permissive Creative Commons license - specifically the "CC Attribution-ShareAlike 3.0 Unported license", see LICENSE file. The required attribution should contain the url of the ChEMBL resource, and also the release version, e.g.:

    https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/README · README · 核实于 2026-11-13

  • ChEMBL 在 ACTIVITIES.data_validity_comment 中标记可疑活性值（如“超出典型范围”“该类型的非标准单位”“可能的转录错误”“可能的作者错误”），由用户决定是否保留。
    chembl.gitbook.io · 2026-11-13

    The use of the flag will allow users to decide whether or not to retain those values in their results set after running a search on the interface or using the downloaded database.

    https://chembl.gitbook.io/chembl-interface-documentation/frequently-asked-questions/chembl-data-questions · 数据集页面 · 核实于 2026-11-13

• 网页接口ebi.ac.uk XML · JSON · YAML · SVG · SDF

  条款同本卡许可。

  • 文本说明 GET 参数必须编码进 URL，且 URL 长度有限，因此 POST 请求通常更方便。
    chembl.gitbook.io · 2026-11-13

    In GET request all the parameters has to be encoded into URL. Because there is a limitation of how long a URL can be it's often more convenient to use POST requests instead.

    https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services · 数据集页面 · 核实于 2026-11-13

• 批量下载chembl.gitbook.io turtle

  条款同本卡许可。

• 网页接口chembl.gitbook.io

  条款同本卡许可。

• 数据库转储ftp.ebi.ac.uk

  条款同本卡许可。

• 仅网页界面chembl.gitbook.io

  条款同本卡许可。

版本

• 最新文本说明 ChEMBL 的版本为 chembl_37。
  ftp.ebi.ac.uk · 2026-11-13

  ChEMBL data is from http://www.ebi.ac.uk/chembl - the version of ChEMBL is chembl_37.

  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/README · README · 核实于 2026-11-13

• 破坏性变更版本间存在表结构变更：ChEMBL 37 弃用 CURATION_LOOKUP、PROTEIN_CLASS_SYNONYMS 两张表及 CELL_DICTIONARY.CL_LINCS_ID、ASSAYS.CURATED_BY 两个字段，新增 ACTIVITIES.MODALITY。
  ftp.ebi.ac.uk · 2026-11-13

  # Tables that have been deprecated since ChEMBL 36: CURATION_LOOKUP PROTEIN_CLASS_SYNONYMS

  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_37_release_notes.txt · official-release-notes · 核实于 2026-11-13

• 破坏性变更ChEMBL 36 因对 ATC、BNF 来源采用更严格的“已批准”解释，已上市药物（MAX_PHASE）数量大幅变化；ChEMBL 37 经人工核对又将 169 个化合物恢复为 MAX_PHASE 4，官方称近期版本间仍会有差异。
  ftp.ebi.ac.uk · 2026-11-13

  Differences in ATC MAX_PHASE will still exist between recent ChEMBL releases, as this curation effort is ongoing.

  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_37_release_notes.txt · official-release-notes · 核实于 2026-11-13

已知缺陷与常见误用

• ChEMBL 在 potential_duplicate 列中标记可能是对早先测量的重复引用。
  chembl.gitbook.io · 2026-11-13

  Identification of potential duplicate values - where an activity measurement is likely to be a repeat citation of an earlier measurement, rather than an independent measurement (flagged using the potential_duplicate column).

  https://chembl.gitbook.io/chembl-interface-documentation/frequently-asked-questions/chembl-data-questions · 数据集页面 · 核实于 2026-11-13

• Landrum 与 Riniker：以最低限度筛选合并 ChEMBL 不同测定的 IC50，一致性差（约 65% 的成对数据相差 >0.3 个对数单位，27% 相差 >1）；严格匹配测定元数据可减轻但不能消除噪声，Ki 也有类似噪声。
  pmc.ncbi.nlm.nih.gov · 2026-11-13

  IC 50 assays selected using minimal curation settings have poor agreement with each other: almost 65% of the points differ by more than 0.3 log units, 27% differ by more than one log unit

  https://pmc.ncbi.nlm.nih.gov/articles/PMC10934815/ · peer-reviewed-paper · 核实于 2026-11-13

• Kalliokoski 等结论较温和：ChEMBL IC50 数据的标准差只比 Ki 大约 25%，混合不同测定的 IC50 只增加中等程度的噪声。
  pmc.ncbi.nlm.nih.gov · 2026-11-13

  The standard deviation of IC 50 data is only 25% larger than the standard deviation of K i data, suggesting that mixing IC 50 data from different assays, even not knowing assay conditions details, only adds a moderate amount of noise to the overall data.

  https://pmc.ncbi.nlm.nih.gov/articles/PMC3628986/ · peer-reviewed-paper · 核实于 2026-11-13

• Kramer 等发现 ChEMBL 的 Ki 数据含单位转录错误、未区分的立体异构体与重复引用（占全部成对数据的 90%），估计实验不确定性决定的 R² 上限约 0.81。
  pubmed.ncbi.nlm.nih.gov · 2026-11-13

  Careful filtering of the data was required because ChEMBL contains unit-transcription errors, undifferentiated stereoisomers, and repeated citations of single measurements (90% of all pairs).

  https://pubmed.ncbi.nlm.nih.gov/22643060/ · peer-reviewed-paper · 核实于 2026-11-13

• ChEMBL 37 在 BindingDB 与 SureChEMBL 专利来源内部及之间发现并去除 13 份重复文献。
  ftp.ebi.ac.uk · 2026-11-13

  13 intra-source and inter-source duplicate documents were identified.

  https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_37_release_notes.txt · official-release-notes · 核实于 2026-11-13

适合的任务

• 文本说明子结构与相似性 Web 服务资源可用于检索 ChEMBL 的化学内容。
  chembl.gitbook.io · 2026-11-13

  The 'Substructure' and 'Similarity' web service resources allow for the chemical content of ChEMBL to be searched.

  https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services · 数据集页面 · 核实于 2026-11-13

• Landrum 与 Riniker 提醒：把不同测定的文献 IC50 合并成一个机器学习数据集在科学上有风险，对 ChEMBL 这类大型文献集合尤甚。
  pmc.ncbi.nlm.nih.gov · 2026-11-13

  the risks of assays being incompatible are even higher when pulling data from large collections of literature data like ChEMBL.

  https://pmc.ncbi.nlm.nih.gov/articles/PMC10934815/ · peer-reviewed-paper · 核实于 2026-11-13

不适合的任务

• 文本说明 Image 资源与其他资源不同，不接受过滤和分页参数。
  chembl.gitbook.io · 2026-11-13

  Unlike the other resources it does not except filtering and paging arguments, but does accept image specific arguments.

  https://chembl.gitbook.io/chembl-interface-documentation/web-services/chembl-data-web-services · 数据集页面 · 核实于 2026-11-13