Chengxin ZHANG1,2
Received:
2025-01-02
Revised:
2025-03-04
Published:
2025-03-06
Contact:
Chengxin ZHANG
张成辛1,2
通讯作者:
张成辛
作者简介:
CLC Number:
Chengxin ZHANG. Challenges and opportunities in text mining-based protein function annotation[J]. Synthetic Biology Journal, DOI: 10.12211/2096-8280.2025-002.
张成辛. 基于文本数据挖掘的蛋白功能预测的机遇与挑战[J]. 合成生物学, DOI: 10.12211/2096-8280.2025-002.
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URL: https://synbioj.cip.com.cn/EN/10.12211/2096-8280.2025-002
Fig. 1 Illustration of Gene Ontology (GO).(a) Three aspects of GO: Molecular Function (MF), Biological Process (BP) and Cellular Component (CC). (b) The chemical reaction catalyzed by the adenylate kinase. (c) The directed acyclic graph (DAG) consisting of the GO term for adenylate kinase activity and its parent GO terms.
Fig. 2 Accumulation of protein entries in the UniProt and Swiss-Prot databases in the past 14 years.(The drop in the number of UniProt proteins in 2015 is caused by removal of redundant microbial proteins, i.e., if two proteins are from different strains or isolates of the same species are almost identical, only one protein is kept.)
证据编码 | 详细解释 |
---|---|
Inferred from Experiment (EXP) | 实验验证的生物功能 |
Inferred from Direct Assay(IDA) | 生物化学或细胞生物学实验验证的生物功能 |
Inferred from Physical Interaction(IPI) | 实验验证的蛋白-蛋白、蛋白-核酸或蛋白-小分子配体相互作用 |
Inferred from Mutant Phenotype(IMP) | 根据同一个基因的两个等位基因的功能差异推测的生物功能 |
Inferred from Genetic Interaction(IGI) | 涉及两个或以上的基因的序列改变或者表达量改变的实验验证的生物功能 |
Inferred from Expression Pattern(IEP) | 根据基因表达的位置或者基因表达时间推测的生物过程 |
Inferred from High Throughput Experiment(HTP) | 高通量实验验证的生物功能 |
Inferred from High Throughput Direct Assay(HDA) | 高通量生物化学实验或高通量细胞生物学实验验证的生物功能 |
Inferred from High Throughput Mutant Phenotype(HMP) | 根据高通量实验中的一个基因的两个等位基因的功能差异推测的生物功能 |
Inferred from Hight Throughput Genetic Interaction(HGI) | 涉及两个或以上的基因的序列改变或者表达量改变的高通量实验验证的生物功能 |
Inferred from High Throughput Expression Pattern(HEP) | 根据高通量实验中基因表达的位置或者基因表达时间推测的生物过程 |
Inferred from Sequence or structural Similarity (ISS) | 根据序列分析或者结构相似性预测并经过人工审核的生物功能 |
Inferred from Sequence Orthology(ISO) | 根据直系同源关系预测并经过人工审核的生物功能 |
Inferred from Sequence Alignment(ISA) | 根据序列比对预测的生物功能;功能预测与序列比对本身都经过人工审核 |
Inferred from Sequence Model(ISM) | 基于隐式马尔科夫模型(如Pfam)等蛋白家族的统计模型预测并经过人工审核的生物功能 |
Inferred from Genomic Context(IGC) | 根据目标基因在基因组上邻近的其它基因元件预测并经过人工审核的生物功能 |
Inferred from Reviewed Computational Analysis(RCA) | 根据大规模实验数据(如酵母双杂交、质谱、基因芯片)预测或者结合多种类型的数据预测并经过人工审核的生物功能 |
Inferred from Biological aspect of Ancestor(IBA) | 根据系统发生树中的先祖基因的功能推测的后代基因的生物功能 |
Inferred from Biological aspect of Descendant(IBD) | 根据系统发生树中的后代基因的功能推测的先祖基因的生物功能 |
Inferred from Key Residues(IKR) | 根据关键氨基酸残基缺失推测的生物功能缺失 |
Inferred from Rapid Divergence(IRD) | 根据后代基因与先祖基因在进化上的快速分歧推断的生物功能缺失 |
Traceable Author Statement(TAS) | 根据综述文献或者实验文献的介绍或讨论章节中的引用文献总结的生物功能 |
Non-traceable Author Statement(NAS) | 根据文献中没有明确实验依据或引用支持的文字描述总结的生物功能 |
Inferred by Curator(IC) | 根据蛋白的已有功能注释推测的相关生物功能;例如,根据一个真核蛋白的已知功能“RNA聚合酶II活性”推测该蛋白应具有功能注释“细胞核” |
Inferred from Electronic Annotation(IEA) | 无人工审核的计算预测得到的生物功能 |
Tab. 1 Evidence codes used for Gene Ontology annotation
证据编码 | 详细解释 |
---|---|
Inferred from Experiment (EXP) | 实验验证的生物功能 |
Inferred from Direct Assay(IDA) | 生物化学或细胞生物学实验验证的生物功能 |
Inferred from Physical Interaction(IPI) | 实验验证的蛋白-蛋白、蛋白-核酸或蛋白-小分子配体相互作用 |
Inferred from Mutant Phenotype(IMP) | 根据同一个基因的两个等位基因的功能差异推测的生物功能 |
Inferred from Genetic Interaction(IGI) | 涉及两个或以上的基因的序列改变或者表达量改变的实验验证的生物功能 |
Inferred from Expression Pattern(IEP) | 根据基因表达的位置或者基因表达时间推测的生物过程 |
Inferred from High Throughput Experiment(HTP) | 高通量实验验证的生物功能 |
Inferred from High Throughput Direct Assay(HDA) | 高通量生物化学实验或高通量细胞生物学实验验证的生物功能 |
Inferred from High Throughput Mutant Phenotype(HMP) | 根据高通量实验中的一个基因的两个等位基因的功能差异推测的生物功能 |
Inferred from Hight Throughput Genetic Interaction(HGI) | 涉及两个或以上的基因的序列改变或者表达量改变的高通量实验验证的生物功能 |
Inferred from High Throughput Expression Pattern(HEP) | 根据高通量实验中基因表达的位置或者基因表达时间推测的生物过程 |
Inferred from Sequence or structural Similarity (ISS) | 根据序列分析或者结构相似性预测并经过人工审核的生物功能 |
Inferred from Sequence Orthology(ISO) | 根据直系同源关系预测并经过人工审核的生物功能 |
Inferred from Sequence Alignment(ISA) | 根据序列比对预测的生物功能;功能预测与序列比对本身都经过人工审核 |
Inferred from Sequence Model(ISM) | 基于隐式马尔科夫模型(如Pfam)等蛋白家族的统计模型预测并经过人工审核的生物功能 |
Inferred from Genomic Context(IGC) | 根据目标基因在基因组上邻近的其它基因元件预测并经过人工审核的生物功能 |
Inferred from Reviewed Computational Analysis(RCA) | 根据大规模实验数据(如酵母双杂交、质谱、基因芯片)预测或者结合多种类型的数据预测并经过人工审核的生物功能 |
Inferred from Biological aspect of Ancestor(IBA) | 根据系统发生树中的先祖基因的功能推测的后代基因的生物功能 |
Inferred from Biological aspect of Descendant(IBD) | 根据系统发生树中的后代基因的功能推测的先祖基因的生物功能 |
Inferred from Key Residues(IKR) | 根据关键氨基酸残基缺失推测的生物功能缺失 |
Inferred from Rapid Divergence(IRD) | 根据后代基因与先祖基因在进化上的快速分歧推断的生物功能缺失 |
Traceable Author Statement(TAS) | 根据综述文献或者实验文献的介绍或讨论章节中的引用文献总结的生物功能 |
Non-traceable Author Statement(NAS) | 根据文献中没有明确实验依据或引用支持的文字描述总结的生物功能 |
Inferred by Curator(IC) | 根据蛋白的已有功能注释推测的相关生物功能;例如,根据一个真核蛋白的已知功能“RNA聚合酶II活性”推测该蛋白应具有功能注释“细胞核” |
Inferred from Electronic Annotation(IEA) | 无人工审核的计算预测得到的生物功能 |
方法 | 功能预测的信息来源(特征) | 机器学习模型 |
---|---|---|
GOtcha、Blast2GO、BAR+ | BLASTp搜索得到的同源序列 | 无 |
ConFunc、PFP、GoFDR | PSI-BLAST搜索得到的同源序列 | 无 |
HFSP | MMseqs2搜索得到的同源序列 | 无 |
ProFunc | BLASTp搜索得到的同源序列、SSM与Jess结构搜索得到的相似结构 | 无 |
COFACTOR | BLASTp与PSI-BLAST搜索得到的同源序列、TM-align结构搜索得到的相似结构、蛋白-蛋白相互作用 | 无 |
MetaGO | BLASTp与PSI-BLAST搜索得到的同源序列、TM-align结构搜索得到的相似结构、蛋白蛋白相互作用 | 逻辑回归 |
StarFunc | BLASTp搜索得到的同源序列、Foldseek与TM-align结构搜索得到的相似结构、Pfam蛋白结构域家族、蛋白-蛋白相互作用、目标蛋白序列(ESM蛋白语言模型提取的特征) | 逻辑回归、全连接神经网络、随机森林 |
DeepFRI、Struct2Go | 三维结构提取的残基接触图、目标蛋白序列(独热编码) | 图卷积神经网络 |
TALE-cmap | 三维结构提取的残基接触图、多序列比对(ESM-MSA蛋白语言模型提取的特征) | Transformer |
CLEAN-Contact | 三维结构提取的残基接触图、目标蛋白序列(ESM蛋白语言模型提取的特征) | 卷积神经网络 |
MS-kNN | 同源序列、基因表达谱、蛋白-蛋白相互作用 | k-最近邻 |
INGA | BLASTp搜索得到的同源序列、蛋白-蛋白相互作用、Pfam蛋白结构域家族 | 无 |
GOLabeler | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、目标蛋白序列(连续三个氨基酸残基序列片段的频率、ProFET程序提取的序列特征) | 逻辑回归、梯度增强树 |
NetGO | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、蛋白-蛋白互作、目标蛋白序列(连续三个氨基酸残基序列片段的频率、ProFET程序提取的序列特征) | 逻辑回归、梯度增强树 |
NetGO2.0 | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、蛋白-蛋白互作、目标蛋白序列(连续三个氨基酸残基序列片段的频率、独热编码)、PubMed摘要 | 逻辑回归、双向长短期记忆神经网络、梯度增强树 |
DeepGO、DeepGOplus、ProteInfer、DeepEC、ECPICK | 目标蛋白序列(独热编码) | 卷积神经网络 |
ATGO+ | BLASTp搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
InterLabelGO+ | DIAMOND搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
DeepGO-SE | 目标蛋白序列(ESM蛋白语言模型提取的特征)、蛋白-蛋白相互作用 | 全连接神经网络、图注意力网络 |
DeepECtransformer | DIAMOND搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 注意力网络 |
CLEAN | 目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
Tab. 2 Existing methods for protein function prediction
方法 | 功能预测的信息来源(特征) | 机器学习模型 |
---|---|---|
GOtcha、Blast2GO、BAR+ | BLASTp搜索得到的同源序列 | 无 |
ConFunc、PFP、GoFDR | PSI-BLAST搜索得到的同源序列 | 无 |
HFSP | MMseqs2搜索得到的同源序列 | 无 |
ProFunc | BLASTp搜索得到的同源序列、SSM与Jess结构搜索得到的相似结构 | 无 |
COFACTOR | BLASTp与PSI-BLAST搜索得到的同源序列、TM-align结构搜索得到的相似结构、蛋白-蛋白相互作用 | 无 |
MetaGO | BLASTp与PSI-BLAST搜索得到的同源序列、TM-align结构搜索得到的相似结构、蛋白蛋白相互作用 | 逻辑回归 |
StarFunc | BLASTp搜索得到的同源序列、Foldseek与TM-align结构搜索得到的相似结构、Pfam蛋白结构域家族、蛋白-蛋白相互作用、目标蛋白序列(ESM蛋白语言模型提取的特征) | 逻辑回归、全连接神经网络、随机森林 |
DeepFRI、Struct2Go | 三维结构提取的残基接触图、目标蛋白序列(独热编码) | 图卷积神经网络 |
TALE-cmap | 三维结构提取的残基接触图、多序列比对(ESM-MSA蛋白语言模型提取的特征) | Transformer |
CLEAN-Contact | 三维结构提取的残基接触图、目标蛋白序列(ESM蛋白语言模型提取的特征) | 卷积神经网络 |
MS-kNN | 同源序列、基因表达谱、蛋白-蛋白相互作用 | k-最近邻 |
INGA | BLASTp搜索得到的同源序列、蛋白-蛋白相互作用、Pfam蛋白结构域家族 | 无 |
GOLabeler | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、目标蛋白序列(连续三个氨基酸残基序列片段的频率、ProFET程序提取的序列特征) | 逻辑回归、梯度增强树 |
NetGO | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、蛋白-蛋白互作、目标蛋白序列(连续三个氨基酸残基序列片段的频率、ProFET程序提取的序列特征) | 逻辑回归、梯度增强树 |
NetGO2.0 | BLASTp搜索得到的同源序列、InterPro蛋白结构域家族、蛋白-蛋白互作、目标蛋白序列(连续三个氨基酸残基序列片段的频率、独热编码)、PubMed摘要 | 逻辑回归、双向长短期记忆神经网络、梯度增强树 |
DeepGO、DeepGOplus、ProteInfer、DeepEC、ECPICK | 目标蛋白序列(独热编码) | 卷积神经网络 |
ATGO+ | BLASTp搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
InterLabelGO+ | DIAMOND搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
DeepGO-SE | 目标蛋白序列(ESM蛋白语言模型提取的特征)、蛋白-蛋白相互作用 | 全连接神经网络、图注意力网络 |
DeepECtransformer | DIAMOND搜索得到的同源序列、目标蛋白序列(ESM蛋白语言模型提取的特征) | 注意力网络 |
CLEAN | 目标蛋白序列(ESM蛋白语言模型提取的特征) | 全连接神经网络 |
Fig. 4 Text mining-based protein GO term prediction in NetGO2.0.(a) LR-Text, the text mining model in NetGO2.0. (b) The architecture of Doc2Vec, which is used as one of the text feature generation methods in LR-Text. In this example, the Doc2Vec neural network model is trained to predict the masked word "jump" given its context in the sentence "The quick brown fox ___ over the lazy dog." The word "the" is excluded from the input sentence as it does not have meaningful information.
Fig. 6 Year of publication for the 8935 PubMed citations newly added to UniProt in 2024.(The 549 papers published in or before year 1999 are not shown.)
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