Python get_name Exemples

Exemple #1

def get_common_ancestors(id1, id2):
    e1 = ssm.get_id(id1.replace(":", "_"))
    e2 = ssm.get_id(id2.replace(":", "_"))
    #print(id1, id2, e1, e2)
    a = ssm.common_ancestors(e1, e2)
    a = [ssm.get_name(x) for x in a]
    return a

Exemple #2

Fichier : parse_biocreative_v_cdr.py Projet : kmkwon94/ainized-biont

def get_common_ancestors(id1, id2):
    """

    :param id1:
    :param id2:
    :return:
    """

    if id1.startswith('CHEBI'):
        ssm.semantic_base('bin/DiShIn/chebi.db')
    if id1.startswith('HP'):
        ssm.semantic_base('bin/DiShIn/hp.db')
    if id1.startswith('GO'):
        ssm.semantic_base('bin/DiShIn/go.db')
    if id1.startswith('DOID'):
        ssm.semantic_base('bin/DiShIn/doid.db')

    e1 = ssm.get_id(id1.replace(':', '_'))

    if id2.startswith('CHEBI'):
        ssm.semantic_base('bin/DiShIn/chebi.db')
    if id2.startswith('HP'):
        ssm.semantic_base('bin/DiShIn/hp.db')
    if id2.startswith('GO'):
        ssm.semantic_base('bin/DiShIn/go.db')
    if id2.startswith('DOID'):
        ssm.semantic_base('bin/DiShIn/doid.db')

    e2 = ssm.get_id(id2.replace(':', '_'))

    a = ssm.common_ancestors(e1, e2)
    a = [ssm.get_name(x) for x in a]

    return a

Exemple #3

def get_path_to_root(id1):
    global chebi_cache
    if id1 in chebi_cache:
        #logging.info("using chebi cache")
        return chebi_cache[id1]
    else:
        e1 = ssm.get_id(id1.replace(":", "_"))
        a = ssm.common_ancestors(e1, e1)
        a = [ssm.get_name(x) for x in a]
        chebi_cache[id1] = a
    return a

Exemple #4

def get_common_ancestors(id1, id2):
    global chebi_cache
    if (id1, id2) in chebi_cache:
        #logging.info("using chebi cache")
        return chebi_cache[(id1, id2)]
    else:
        e1 = ssm.get_id(id1.replace(":", "_"))
        e2 = ssm.get_id(id2.replace(":", "_"))
        #print(id1, id2, e1, e2)
        a = ssm.common_ancestors(e1, e2)
        a = [ssm.get_name(x) for x in a]
        chebi_cache[(id1, id2)] = a
        return a

Exemple #5

Fichier : parse_xml.py Projet : kmkwon94/ainized-biont

def get_path_to_root(entity_id):
    """

    :param entity_id:
    :return:
    """

    if entity_id.startswith('CHEBI'):
        ssm.semantic_base('bin/DiShIn/chebi.db')
    if entity_id.startswith('HP'):
        ssm.semantic_base('bin/DiShIn/hp.db')
    if entity_id.startswith('GO'):
        ssm.semantic_base('bin/DiShIn/go.db')
    if entity_id.startswith('DOID'):
        ssm.semantic_base('bin/DiShIn/doid.db')

    e1 = ssm.get_id(entity_id.replace(':', '_'))

    a = ssm.common_ancestors(e1, e1)
    a = [ssm.get_name(x) for x in a]

    return a

Exemple #6

def get_path_to_root(id1):
    e1 = ssm.get_id(id1.replace(":", "_"))
    a = ssm.common_ancestors(e1, e1)
    a = [ssm.get_name(x) for x in a]
    return a

Exemple #7

Fichier : generate_chebi_pop.py Projet : pedroruas18/PPRSSM

import os
import xml.etree.ElementTree as ET
from chebi_ssm import get_best_chebi_id
import sys
sys.path.append("./")

from DiShIn import ssm
ssm.semantic_base("DiShIn/chebi.db")

chebi_ids = list(ssm.connection.execute("SELECT id FROM entry"))
with open("chebi_pop", 'w') as f:
    for cid in chebi_ids:
        name = ssm.get_name(cid[0]).replace("_", ':')
        if name.startswith("CHEBI"):

            ic = ssm.information_content_extrinsic(cid[0])
            #ic = ssm.information_content_intrinsic(cid[0])
            if ic != 0:
                ic = 1 / ic
            f.write("url:{}\t{}\n".format(name.replace("CHEBI", "http"), ic))