MappingProviderInterface Examples

[1]:


%reset -f

Import libraries

[9]:

import sys
import os
from oaklib.selector import get_resource_from_shorthand
from oaklib.utilities.mapping.sssom_utils import StreamingSssomWriter
from oaklib.cli import lexmatch
from oaklib.utilities.lexical.lexical_indexer import create_lexical_index, lexical_index_to_sssom
import warnings
warnings.filterwarnings('ignore')

Declare variables

[3]:

BIOPORTAL="bioportal:"
OBO="obo"
# NOTE: Make sure you have your unique biportal api-key in a txt file locally.
API_KEY_FILE = "api-key.txt"
limb_curie = "UBERON:0002101"
limb_curie_2 = "MA:0000007"
input_dir = "input"
xao_file = "xao.obo"
ma_file = "ma.obo"

Functions

[14]:

def get_implementation(rsrc:str):
    resource = get_resource_from_shorthand(rsrc)
    oi = resource.implementation_class()

    if rsrc == "bioportal:":
        oi.load_bioportal_api_key(API_KEY_FILE)
    else:
        resource.directory = input_dir
        oi = resource.implementation_class(resource)

    return oi

def render_sssom(rsrc:str, curie:str):
    writer = StreamingSssomWriter(sys.stdout)
    oi = get_implementation(rsrc)
    for m in oi.get_sssom_mappings_by_curie(curie):
        writer.emit(m)

    writer.close()

def get_lexmatch(rsrc:str):
    impl = get_implementation(rsrc)
    ix = create_lexical_index(impl)
    msdf = lexical_index_to_sssom(impl, ix)
    return msdf.df

Part 1

Bioportal => SSSOM

[5]:

render_sssom(BIOPORTAL, limb_curie)

# curie_map: {}
# license: UNSPECIFIED
# mapping_set_id: temp
subject_id      predicate_id    object_id       match_type      mapping_provider        mapping_tool
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4f49aa6124b587b96b0404c5deaa6c0469c62698    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:exactMatch http://purl.obolibrary.org/obo/UBERON_0002101   Unspecified     http://data.bioontology.org/metadata/Mapping    SAME_URI
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/4516e5ffbeb793c8c61039c695023423951699f5    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/fa4cdef7fec35673b3dee1834bbbe8ed841b3d48    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.bioontology.org/ontology/CSP/2715-5305      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12429       Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/d7ca07679d2a01092ddaa57a481807e860675703    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/d7ca07679d2a01092ddaa57a481807e860675703    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch https://cadsr.nci.nih.gov/metadata/CADSR-VS/d7ca07679d2a01092ddaa57a481807e860675703    Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
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http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/NCIT_C12429      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/NCIT_C12429      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/BTO_0001492      Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM
http://purl.obolibrary.org/obo/UBERON_0002101   skos:closeMatch http://purl.obolibrary.org/obo/VHOG_0000336     Unspecified     http://data.bioontology.org/metadata/Mapping    LOOM

Local Ontology => SSSOM

[6]:

# Xenopus Anatomy Ontology
render_sssom(xao_file, limb_curie)

# curie_map: {}
# license: UNSPECIFIED
# mapping_set_id: temp
subject_id      predicate_id    object_id       match_type
XAO:0003027     skos:closeMatch UBERON:0002101  Unspecified

[7]:

# Mouse adult gross anatomy
render_sssom(ma_file, limb_curie_2)

# curie_map: {}
# license: UNSPECIFIED
# mapping_set_id: temp
subject_id      predicate_id    object_id       match_type
MA:0000007      skos:closeMatch EMAPS:1640528   Unspecified

Part 2

Get mappings using `lexmatch`

[15]:

get_lexmatch(xao_file)

[15]:

	subject_id	subject_label	predicate_id	object_id	object_label	match_type	mapping_tool	subject_match_field	object_match_field	match_string
0	XAO:0000006	otic vesicle	skos:closeMatch	XAO:0000189	auditory apparatus	Lexical	oaklib	oio:hasBroadSynonym	oio:hasBroadSynonym	ear
1	XAO:0000006	otic vesicle	skos:closeMatch	XAO:0000223	otic placode	Lexical	oaklib	oio:hasBroadSynonym	oio:hasBroadSynonym	ear
2	XAO:0000008	lens	skos:closeMatch	XAO:0005240	regenerating lens	Lexical	oaklib	rdfs:label	oio:hasBroadSynonym	lens
3	XAO:0000021	ventricular zone	skos:closeMatch	XAO:0004616	ventrolateral neural tube	Lexical	oaklib	rdfs:label	oio:hasBroadSynonym	ventricular zone
4	XAO:0000023	skin	skos:closeMatch	XAO:0000028	epidermis	Lexical	oaklib	rdfs:label	oio:hasBroadSynonym	skin
...	...	...	...	...	...	...	...	...	...	...
99	XAO:0004609	neural nucleus	skos:closeMatch	XAO:0005038	nucleus	Lexical	oaklib	oio:hasBroadSynonym	rdfs:label	nucleus
100	XAO:0005072	skin mucous gland	skos:closeMatch	XAO:0005073	mucous gland	Lexical	oaklib	oio:hasBroadSynonym	rdfs:label	mucous gland
101	XAO:0005084	blastomere D1	skos:closeMatch	XAO:0005100	blastomere D2.1.1	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	D1
102	XAO:0005085	blastomere D2	skos:closeMatch	XAO:0005102	blastomere D2.2.1	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	D2
103	XAO:0005322	tadpole	skos:closeMatch	XAO:1000008	tadpole stage	Lexical	oaklib	rdfs:label	oio:hasExactSynonym	tadpole

104 rows × 10 columns

[16]:

get_lexmatch(ma_file)

[16]:

	subject_id	subject_label	predicate_id	object_id	object_label	match_type	mapping_tool	subject_match_field	object_match_field	match_string
0	MA:0000004	trunk	skos:closeMatch	MA:0000020	back of trunk	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	body
1	MA:0000133	cerebral hemisphere	skos:closeMatch	MA:0000183	telencephalon	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	cerebrum
2	MA:0000185	cerebral cortex	skos:closeMatch	MA:0002754	neocortex	Lexical	oaklib	rdfs:label	oio:hasRelatedSynonym	cerebral cortex
3	MA:0000193	olfactory cortex	skos:closeMatch	MA:0002413	olfactory lobe	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	olfactory lobe
4	MA:0000318	viscerocranium	skos:closeMatch	MA:0003159	facial bone	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	facial bone
5	MA:0000341	oral region	skos:closeMatch	MA:0002474	mouth	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	mouth
6	MA:0000402	coagulating gland	skos:closeMatch	MA:0002422	prostate gland anterior lobe	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	prostate gland anterior lobe
7	MA:0000744	lymph node secondary follicle	skos:closeMatch	MA:0002989	lymph node germinal center	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	lymph node germinal center
8	MA:0000999	cerebellum vermis lobule II	skos:closeMatch	MA:0001000	cerebellum vermis lobule III	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	central lobule
9	MA:0001001	cerebellum vermis lobule IV	skos:closeMatch	MA:0001002	cerebellum vermis lobule V	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	culmen
10	MA:0001344	central carpal bone	skos:closeMatch	MA:0001349	navicular	Lexical	oaklib	oio:hasRelatedSynonym	oio:hasRelatedSynonym	centrale
11	MA:0001722	decidua	skos:closeMatch	MA:0002905	decidua basalis	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	decidua basalis
12	MA:0001823	respiratory system epithelium	skos:closeMatch	MA:0001827	respiratory system mucosa	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	respiratory system mucosa
13	MA:0002324	intercostales	skos:closeMatch	MA:0003165	intercostal muscle	Lexical	oaklib	oio:hasRelatedSynonym	rdfs:label	intercostal muscle

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