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feat(data): add MacrolactoneDB data directory with ml_id column

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- Add MacrolactoneDB filtered datasets
- Add ring12_20 and ring16 subdirectories with processed data
- Add ml_id column as unique identifier (ML00000001 format)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
lingyuzeng
2026-03-19 11:43:45 +08:00
parent 13dd336e37
commit 360cbc487e
10 changed files with 308289 additions and 0 deletions
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data/MacrolactoneDB/MacrolactoneDB_Filtered_with_Reported_Activity_2751.csv Normal file
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data/MacrolactoneDB/Macrolactone_Filtered_16Ring_Active_435.csv Normal file
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data/MacrolactoneDB/README.md Normal file
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website: https://macrolact.collaborationspharma.com/
通过MacrolactoneDB页面筛选的结果并不准确，我限定16环，但是在下载的csv里面有14环的结果，所以还是要自己进行在筛选一遍。

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data/MacrolactoneDB/ring12_20/README.md Normal file
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Your Filtered Macrolactone Database
11036 compounds have been filtered from MacrolactoneDB based on your specified inputs.

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data/MacrolactoneDB/ring12_20/counts.txt Normal file
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Target Organisms
Homo sapiens 815
Homo sapiens, None 180
Plasmodium falciparum 161
Hepatitis C virus, None 112
Homo sapiens, Plasmodium falciparum 63
Oryctolagus cuniculus 62
Mus musculus 60
Toxoplasma gondii 39
Homo sapiens, Rattus norvegicus 27
Mus musculus, Homo sapiens 24
None, Rattus norvegicus 23
Human immunodeficiency virus 1 20
Hepatitis C virus 18
Rattus norvegicus 17
Homo sapiens, Sus scrofa 11
Homo sapiens, Chlorocebus aethiops 10
Serratia marcescens 9
Escherichia coli 8
Oryctolagus cuniculus, Homo sapiens 7
Streptococcus pneumoniae 6
Oryctolagus cuniculus, Staphylococcus aureus, Raoultella planticola, Bacillus subtilis, Mus musculus, Micrococcus luteus, None, Escherichia coli, Plasmodium falciparum, Streptococcus pneumoniae, Homo sapiens, Escherichia coli K-12, Toxoplasma gondii 6
Plasmodium falciparum K1 5
Bacillus anthracis 5
Mus musculus, Homo sapiens, None 5
Bacillus anthracis, Homo sapiens 4
Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus 4
Mus musculus, None 4
Plasmodium falciparum, Homo sapiens, None 4
None, Homo sapiens, Plasmodium falciparum 3
Bacillus subtilis, Homo sapiens 3
Oryctolagus cuniculus, Homo sapiens, None 3
Sus scrofa, Mus musculus, None, Plasmodium falciparum, Homo sapiens, Rattus norvegicus 2
Homo sapiens, None, Rattus norvegicus 2
Cryptococcus neoformans 2
Homo sapiens, None, Chlorocebus aethiops 2
Staphylococcus aureus 2
Candida albicans, Cryptococcus neoformans, Mycobacterium intracellulare, Aspergillus fumigatus 2
Mus musculus, None, Human immunodeficiency virus 1 2
Escherichia coli (strain K12) 2
Plasmodium falciparum 3D7, Homo sapiens 2
Aspergillus fumigatus 1
Sus scrofa 1
Saccharomyces cerevisiae S288c, Human immunodeficiency virus 1, Human herpesvirus 1, Plasmodium falciparum, None, Homo sapiens, Rattus norvegicus 1
Hepatitis C virus, Homo sapiens, None 1
Plasmodium falciparum 3D7 1
Bacillus subtilis 1
Mus musculus, Homo sapiens, None, Saccharomyces cerevisiae 1
Chlorocebus aethiops 1
Homo sapiens, Escherichia coli K-12, None 1
Hepatitis C virus, Homo sapiens, None, Rattus norvegicus 1
None, Homo sapiens, Human herpesvirus 1 1
Homo sapiens, None, Trypanosoma brucei brucei 1
Homo sapiens, None, Cryptococcus neoformans 1
Homo sapiens, Rattus norvegicus, Human immunodeficiency virus 1 1
None, Plasmodium falciparum, Escherichia coli, Streptococcus pneumoniae, Naegleria fowleri, Homo sapiens, Streptococcus, Toxoplasma gondii 1
Giardia intestinalis, Trypanosoma cruzi, Equus caballus, Bos taurus, Mus musculus, None, Plasmodium falciparum, Chlorocebus aethiops, Homo sapiens 1
Plasmodium falciparum NF54, Trypanosoma cruzi, Trypanosoma brucei rhodesiense, Rattus norvegicus 1
None, Homo sapiens, Plasmodium falciparum K1, Plasmodium falciparum 1
Saccharomyces cerevisiae S288c, Homo sapiens, None, Saccharomyces cerevisiae, Phytophthora sojae 1
Bacillus subtilis, Homo sapiens, Schistosoma mansoni, Saccharomyces cerevisiae, Giardia intestinalis 1
Streptococcus, Homo sapiens, None 1
Mus musculus, Homo sapiens, Rattus norvegicus 1
Homo sapiens, Spinacia oleracea 1
Human immunodeficiency virus 1, Mus musculus, None, Hepatitis C virus, Homo sapiens, Rattus norvegicus 1
None, Plasmodium falciparum, Trypanosoma brucei rhodesiense 1
Hepatitis C virus, None, Rattus norvegicus 1
Homo sapiens, Equus caballus 1
Plasmodium falciparum NF54, Trypanosoma cruzi, Trypanosoma brucei rhodesiense 1
Schistosoma mansoni, Influenza A virus 1
Leishmania chagasi, Trypanosoma cruzi 1
Candida albicans, Cryptococcus neoformans 1
None, Plasmodium falciparum 1
Caenorhabditis elegans 1
Bos taurus, Sus scrofa 1
Plasmodium falciparum, Enterococcus faecium 1
Homo sapiens, Gallus gallus 1
Homo sapiens, Escherichia coli 1
Plasmodium falciparum, Homo sapiens, None, Rattus norvegicus, Schistosoma mansoni 1
Homo sapiens, None, Influenza A virus 1
Mycobacterium tuberculosis, None 1
Escherichia coli, Homo sapiens, Toxoplasma gondii, None, Streptococcus pneumoniae 1
Bacillus subtilis, Oryctolagus cuniculus, Homo sapiens, Schistosoma mansoni, Giardia intestinalis 1
Homo sapiens, None, Rattus norvegicus, Escherichia coli O157:H7 1
Giardia intestinalis, Schistosoma mansoni, Mus musculus, None, Homo sapiens, Saccharomyces cerevisiae 1
Trypanosoma cruzi 1
Influenza A virus 1
Escherichia coli K-12 1
Human herpesvirus 4 (strain B95-8) 1

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data/MacrolactoneDB/ring12_20/processed_embedding_small.csv Normal file
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