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kipoi / models

Model zoo for genomics
http://kipoi.org
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Add the TF name to DeepBind models #91

Closed Avsecz closed 6 years ago

Avsecz commented 6 years ago 
# The index has the following fields:
#
#   ID: A unique id of the form 01234.567 that identifies a model 
#       01234 is unique for each combination of (Protein, Species), and 567 is unique 
#       for each combination of (Experiment, Experiment Details, Model ID),
#       In other words, 01234 identifies the protein 'version', whereas 567 identifies 
#       the model 'version' for that protein version.
#   Protein: The protein name, e.g. RBFOX1.
#   Type: Indicates whether the protein is considered an RBP, a TF, etc.
#   Species: The species name, e.g. Homo sapiens.
#   Family: The protein family, e.g. Homeodomain.
#   Class: The protein structural class, e.g. Zinc-coordinating.
#   Experiment: The technology used to measure the training data, e.g. ChIP-seq, HT-SELEX.
#   Experiment Details: A list of strings that describe how the experiment was configured,
#                       e.g. ["Cell Line=K562","Lab=Stanford"]
#   Model ID: A number/string that can be used to identify this model as distinct from 
#             other models for the same (Protein, Species, Experiment, Experiment Details),
#             e.g. if a new, better model was trained and therefore needs a new version ID.
#   Comments: 
#
#
ID  Protein Type    Species Family  Class   Experiment  Experiment Details  Model   Cite    Labels  Path    Comment
D00001.001  Cebpb   TF  Mus musculus    bZIP        PBM ['DREAM5ID=C_1', 'Array=HK']    deepbind 0.1    PMID 23354101       E:/Results/deepbind/dream5/final/C_1    
D00002.001  Egr2    TF  Mus musculus    C2H2 ZF     PBM ['DREAM5ID=C_2', 'Array=HK']    deepbind 0.1    PMID 23354101       E:/Results/deepbind/dream5/final/C_2    
D00003.001  Esr1    TF  Mus musculus    Nuclear receptor        PBM ['DREAM5ID=C_3', 'Array=HK']    deepbind 0.1    PMID 23354101       E:/Results/deepbind/dream5/final/C_3
Avsecz commented 6 years ago

use this table: https://github.com/kundajelab/DeepBindToKeras/blob/master/deepbind_db/db.tsv