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Listing the Samples registered into DeepBlue
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# Samples | |
# DeepBlue organizes the Biological Names into BioSources and Samples. | |
# While the BioSources are the biological entities, the Samples are the instances of these entities. | |
# For example, the BioSource blood. It refer to any blood, but a blood from a specific donor, time, or caractistic will have be a specific sample. | |
# All Samples refer to a BioSource and a set o attributes, that we name metadata. | |
import xmlrpclib | |
# Before going further, we must set up the client: | |
url = "http://deepblue.mpi-inf.mpg.de/xmlrpc" | |
server = xmlrpclib.Server(url, encoding='UTF-8', allow_none=True) | |
# You can use the anonymous key or your own user key | |
user_key = "anonymous_key" | |
# The command list_samples is used to list all Samples from a given BioSource: | |
server.list_samples("blood", {}, user_key) | |
# Output: | |
# ['okay', | |
# [['s3', | |
# {'_id': 's3', | |
# 'biosource_name': 'blood', | |
# 'description': 'leukemia (UCDavis alternate), "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC', | |
# 'karyotype': 'cancer', | |
# 'lineage': 'mesoderm', | |
# 'organism': 'human', | |
# 'sex': 'F', | |
# 'source': 'ENCODE', | |
# 'term': 'K562b', | |
# 'tier': '1', | |
# 'tissue': 'leukemia (UCDavis alternate), "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC', | |
# 'user': 'Populator'}], | |
# The samples are automatically load from the Epigenetics Projects (BLUEPRINT, ENCODE, Roadmap) | |
# and we are always trying to perform the best match between the mapped BioSource and the Biological Entitiy of the Experiment. | |
# It is important to remid that the metadata key names are not uniformized, so depending the Project or Sample, | |
# there can have different names with the same semantic. It is possible to list only the Knowing the Samples Metadata fields, |
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