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Added HD kgs and opt params of restr OI
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@rosazwart
rosazwart committed Aug 5, 2024
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162 changes: 162 additions & 0 deletions datafetcher.log
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Expand Up @@ -346,3 +346,165 @@ RO:0003304 contributes to condition
RO:HOM0000017 in orthology relationship with
2024-08-01 16:49:30,665 INFO Graph of all connections between concepts saved to restr_oi_concepts.png
2024-08-01 16:49:30,690 INFO List of triplets saved to restr_oi_triples.csv
2024-08-05 10:51:32,890 INFO Created a list of tuples with 96352 entries
2024-08-05 10:51:32,895 INFO Loaded 96352 associations
2024-08-05 10:51:33,493 INFO Created a dataframe with 96352 entries and column values ['id' 'subject_id' 'subject_label' 'subject_iri' 'subject_category'
'subject_taxon_id' 'subject_taxon_label' 'object_id' 'object_label'
'object_iri' 'object_category' 'object_taxon_id' 'object_taxon_label'
'relation_id' 'relation_label' 'relation_iri']
2024-08-05 10:51:34,674 INFO Created a dataframe with 9732 entries and column values ['id' 'semantic_groups' 'name']
2024-08-05 10:52:07,673 INFO Created a list of tuples with 228753 entries
2024-08-05 10:52:07,683 INFO Loaded 228753 associations
2024-08-05 10:52:09,233 INFO Created a dataframe with 228753 entries and column values ['id' 'subject_id' 'subject_label' 'subject_iri' 'subject_category'
'subject_taxon_id' 'subject_taxon_label' 'object_id' 'object_label'
'object_iri' 'object_category' 'object_taxon_id' 'object_taxon_label'
'relation_id' 'relation_label' 'relation_iri']
2024-08-05 10:52:12,586 INFO Created a dataframe with 14618 entries and column values ['id' 'semantic_groups' 'name']
2024-08-05 12:33:35,733 INFO Created a list of tuples with 228753 entries
2024-08-05 12:33:35,743 INFO Loaded 228753 associations
2024-08-05 12:33:35,748 INFO Created a list of tuples with 305 entries
2024-08-05 12:33:35,749 INFO Loaded 305 associations
2024-08-05 12:33:35,754 INFO Created a list of tuples with 39 entries
2024-08-05 12:33:35,754 INFO Loaded 39 associations
2024-08-05 12:33:39,480 INFO The graph contains 7 different semantic groups: {'PHYS', 'GENO', 'ANAT', 'VARI', 'GENE', 'ORTH', 'DISO'}
2024-08-05 12:33:39,481 INFO For the graph, a total of 228655 edges and 14618 nodes have been generated.
2024-08-05 12:33:40,418 INFO The graph contains 8 different semantic groups: {'DRUG', 'PHYS', 'GENO', 'ANAT', 'VARI', 'GENE', 'ORTH', 'DISO'}
2024-08-05 12:33:40,419 INFO For the graph, a total of 228999 edges and 14833 nodes have been generated.
2024-08-05 12:33:40,422 INFO There are 8 semantic groups: ['ORTH' 'DISO' 'GENO' 'DRUG' 'GENE' 'ANAT' 'PHYS' 'VARI']
2024-08-05 12:33:40,484 INFO There are 21 relation labels: relation_label
relation_id
BFO:0000050 is part of
CustomRO:DC is substance that treats
CustomRO:TTD targets
GENO:0000222 has genotype
GENO:0000408 is allele of
GENO:0000418 has affected feature
GENO:0000840 pathogenic for condition
RO:0002200 has phenotype
RO:0002206 expressed in
RO:0002325 colocalizes with
RO:0002326 contributes to
RO:0002327 enables
RO:0002331 involved in
RO:0002434 interacts with
RO:0003301 has role in modeling
RO:0003303 causes condition
RO:0003304 contributes to condition
RO:0004013 is causal germline mutation in
RO:0004016 is causal germline mutation partially giving r...
RO:HOM0000017 in orthology relationship with
RO:HOM0000020 in 1 to 1 orthology relationship with
2024-08-05 12:33:42,106 INFO Graph of all connections between concepts saved to prev_hd_concepts.png
2024-08-05 12:33:42,167 INFO List of triplets saved to prev_hd_triples.csv
2024-08-05 12:40:00,638 INFO Created a list of tuples with 228753 entries
2024-08-05 12:40:00,650 INFO Loaded 228753 associations
2024-08-05 12:40:04,339 INFO The graph contains 12 different semantic groups: {'variant', 'gene', 'interaction', 'model', 'disease', 'phenotype', 'function', 'anatomy', 'pathway', 'marker', 'homology', 'genotype'}
2024-08-05 12:40:04,340 INFO For the graph, a total of 228655 edges and 14618 nodes have been generated.
2024-08-05 12:40:04,355 INFO Extracted a total of 14618 nodes that belong to at least one of the semantic groups []
2024-08-05 12:40:04,413 INFO A total of 14618 gene IDs has been extracted
2024-08-05 12:40:04,532 INFO Loaded 19378 drug-target interactions:
DRUG_NAME STRUCT_ID TARGET_NAME ... ACTION_TYPE TDL ORGANISM
0 levobupivacaine 4 Potassium voltage-gated channel subfamily H me... ... NaN Tclin Homo sapiens
1 levobupivacaine 4 Sodium channel protein type 1 subunit alpha ... NaN Tclin Homo sapiens
2 levobupivacaine 4 Sodium channel protein type 4 subunit alpha ... BLOCKER Tclin Homo sapiens

[3 rows x 20 columns]
2024-08-05 12:40:29,177 INFO For a total of 16141 drug-target interactions, new mapped IDs are found.
2024-08-05 12:40:29,200 INFO Retrieved 316 drug-target interactions with matched gene IDs:
DRUG_NAME STRUCT_ID GENE_ID PROD_ID PROD_NAME
237 adenosine 90 HGNC:4141 P04406 Glyceraldehyde-3-phosphate dehydrogenase liver
257 adenosine triphosphate 91 HGNC:5241 P11142 Heat shock cognate 71 kDa protein
258 adenosine triphosphate 91 HGNC:5232 P0DMV8 Heat shock 70 kDa protein 1A
330 alfentanil 114 HGNC:8156 P35372 Mu-type opioid receptor
2024-08-05 12:40:29,203 INFO Total of 316 drug-target associations changed to 305 by dropping duplicates.
2024-08-05 12:40:30,286 INFO All 610 TTD associations are saved into restr_hd_ttd_associations.csv
2024-08-05 12:40:30,290 INFO Created a list of tuples with 610 entries
2024-08-05 12:40:30,313 INFO Extracted a total of 215 nodes that belong to at least one of the semantic groups ['drug']
2024-08-05 12:40:30,326 INFO Extracted a total of 6440 nodes that belong to at least one of the semantic groups ['disease', 'phenotype']
2024-08-05 12:40:30,353 INFO There are 215 unique drug names
2024-08-05 12:40:30,354 INFO There are 6440 unique disease/phenotype IDs
2024-08-05 12:40:30,735 INFO Loaded 28978 drug-disease pairs:
DRUG_ID DRUG_NAME DISEASE_NAME PHASE
0 D00ABE ald-301 ischemia Phase 2
1 D00ABE ald-301 peripheral arterial disease Phase 2
2 D00ABO kw-2449 acute myeloid leukaemia Phase 1
2024-08-05 12:40:30,772 INFO Loaded 699 phenotypes with matching IDs scoring 80:
Name ontologyTermName ontologyTermIRI score validated review DISEASE_ID
0 respiratory failure Respiratory failure http://purl.obolibrary.org/obo/HP_0002878 100.00 False False HP:0002878
1 sexual dysfunction Male sexual dysfunction http://purl.obolibrary.org/obo/HP_0040307 86.49 False False HP:0040307
6 pollakiuria Pollakisuria http://purl.obolibrary.org/obo/HP_0100515 88.00 False False HP:0100515
2024-08-05 12:40:30,821 INFO Total of 14760 disease names mapped to their IDs:
DRUG_ID DRUG_NAME DISEASE_ID DISEASE_NAME
1 D00ABE ald-301 HP:0004950 peripheral arterial disease
2 D00ABO kw-2449 HP:0004808 acute myeloid leukaemia
4 D00ACC nd1251 HP:0000716 depression
5 D00ACH hmr-4004 HP:0100658 bacterial infection
11 D00AHT prame antigen-specific cancer immunotherapeutic HP:0030358 non small cell lung cancer
12 D00AHT prame antigen-specific cancer immunotherapeutic HP:0030358 non small cell lung cancer
14 D00AHT prame antigen-specific cancer immunotherapeutic HP:0002861 melanoma
19 D00AJS aik11 HP:0005978 non insulin dependent diabetes
21 D00AKQ o-desulfated heparin HP:0006510 chronic obstructive pulmonary disease
22 D00AKR amg 479 HP:0003002 breast cancer
2024-08-05 12:40:30,830 INFO A total of 39 are matched with existing drugs and diseases/phenotypes
2024-08-05 12:40:30,832 INFO Total of 39 drug-disease associations changed to 39 by dropping duplicates.
2024-08-05 12:40:31,006 INFO All DrugCentral associations are saved into restr_hd_drugcentral_associations.csv
2024-08-05 12:40:31,008 INFO Created a list of tuples with 39 entries
2024-08-05 12:40:31,836 INFO The graph contains 14 different semantic groups: {'variant', 'gene', 'interaction', 'model', 'disease', 'phenotype', 'function', 'drug', 'anatomy', 'pathway', 'gene product', 'marker', 'homology', 'genotype'}
2024-08-05 12:40:31,837 INFO For the graph, a total of 229039 edges and 14877 nodes have been generated.
2024-08-05 12:40:31,839 INFO There are 14 semantic groups: ['homology' 'phenotype' 'gene' 'interaction' 'drug' 'function' 'model'
'variant' 'genotype' 'gene product' 'anatomy' 'pathway' 'disease'
'marker']
2024-08-05 12:40:31,884 INFO There are 22 relation labels: relation_label
relation_id
BFO:0000050 is part of
CustomRO:DC is substance that treats
CustomRO:TTD1 is product of
CustomRO:TTD2 targets
GENO:0000222 has genotype
GENO:0000408 is allele of
GENO:0000418 has affected feature
GENO:0000840 pathogenic for condition
RO:0002200 has phenotype
RO:0002206 expressed in
RO:0002325 colocalizes with
RO:0002326 contributes to
RO:0002327 enables
RO:0002331 involved in
RO:0002434 interacts with
RO:0003301 has role in modeling
RO:0003303 causes condition
RO:0003304 contributes to condition
RO:0004013 is causal germline mutation in
RO:0004016 is causal germline mutation partially giving r...
RO:HOM0000017 in orthology relationship with
RO:HOM0000020 in 1 to 1 orthology relationship with
2024-08-05 12:40:32,931 INFO Graph of all connections between concepts saved to all_hd_concepts.png
2024-08-05 12:40:33,002 INFO List of triplets saved to all_hd_triples.csv
2024-08-05 14:04:06,150 INFO The graph contains 11 different semantic groups: {'taxon', 'biological process', 'molecular function', 'gene', 'variant', 'biological artifact', 'disease', 'phenotype', 'drug', 'gene product', 'genotype'}
2024-08-05 14:04:06,151 INFO For the graph, a total of 230228 edges and 14882 nodes have been generated.
2024-08-05 14:04:06,152 INFO There are 11 semantic groups: ['gene' 'phenotype' 'drug' 'molecular function' 'biological artifact'
'taxon' 'variant' 'genotype' 'gene product' 'biological process'
'disease']
2024-08-05 14:04:06,180 INFO There are 19 relation labels: relation_label
relation_id
CustomRO:DC is substance that treats
CustomRO:TTD1 is product of
CustomRO:TTD2 targets
CustomRO:associatedphenotype associated with phenotype
CustomRO:expressesgene expresses gene
CustomRO:foundin found in
CustomRO:isof is of
CustomRO:isvariantin is variant in
GENO:0000222 has genotype
GENO:0000408 is allele of
GENO:0000418 has affected feature
RO:0002325 colocalizes with
RO:0002327 enables
RO:0002331 involved in
RO:0002434 interacts with
RO:0003301 has role in modeling
RO:0003303 causes condition
RO:0003304 contributes to condition
RO:HOM0000017 in orthology relationship with
2024-08-05 14:04:06,547 INFO Graph of all connections between concepts saved to restr_hd_concepts.png
2024-08-05 14:04:06,585 INFO List of triplets saved to restr_hd_triples.csv
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