Look Up table with Embeddings - UniProt - 2025 - Non Computational annotations

This PostgreSQL database contains structured information extracted from the UniProt API (retrieved in April 2025). It includes: 126,582 proteins 123,518 sequences 494.072 embeddings generated with ProtT5, ProSTT5, ESM2, Ankh 623,134 GO term annotations (with evidence codes: EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC) Associated biological metadata The data was extracted using the protein-information-system repository and is used within the FANTASIA pipeline for automated functional annotation of protein sequences. The following UniProt API filter was applied to retrieve annotations:https://www.uniprot.org/uniprotkb?query=%28+go_exp%3A*+OR+go_ida%3A*+OR+go_ipi%3A*+OR+go_imp%3A*+OR+go_igi%3A*+OR+go_iep%3A*+OR+go_tas%3A*+OR+go_ic%3A*%29To ensure embedding reproducibility, all sequences were processed with batch size = 1, avoiding discrepancies caused by padding artifacts common in PLMs like ProtT5. To initialize the database, either of the following methods can be used: Option 1: Using pg_restore pg_restore -U usuario -h localhost -p 5432 -d BioData ./BioData_backup_2025_hq.tar Option 2: Using the FANTASIA CLI fantasia initialize --embeddings_url https://zenodo.org/records/15704357/files/PIS_2025_ankh_exp.tar?download=1 Notes:本PostgreSQL数据库包含从UniProt API提取的结构化信息（于2025年4月获取），其包含以下内容： 1. 126,582条蛋白质记录 2. 123,518条蛋白质序列 3. 494,072个由ProtT5、ProSTT5、ESM2、Ankh生成的嵌入向量（embeddings） 4. 623,134条GO术语注释（GO term），附带证据代码：EXP、IDA、IPI、IMP、IGI、IEP、TAS、IC 关联的生物学元数据 本数据集通过蛋白质信息系统（protein-information-system）代码库提取数据，并在FANTASIA流程中用于蛋白质序列的自动化功能注释。 本次检索应用了如下UniProt API过滤条件：https://www.uniprot.org/uniprotkb?query=%28+go_exp%3A*+OR+go_ida%3A*+OR+go_ipi%3A*+OR+go_imp%3A*+OR+go_igi%3A*+OR+go_iep%3A*+OR+go_tas%3A*+OR+go_ic%3A*%29 为确保嵌入向量的可复现性，所有序列均以批次大小=1进行处理，以避免ProtT5等预训练语言模型（Pre-trained Language Models，简称PLMs）常见的填充伪影引发的结果偏差。 可通过以下任一方式初始化该数据库： 方案1：使用pg_restore工具 pg_restore -U usuario -h localhost -p 5432 -d BioData ./BioData_backup_2025_hq.tar 方案2：使用FANTASIA命令行界面（CLI） fantasia initialize --embeddings_url https://zenodo.org/records/15704357/files/PIS_2025_ankh_exp.tar?download=1 备注：