Closed ramiromagno closed 3 years ago
ens-lgil
commented
3 years ago Dear @ramiromagno ,
A new parameter include_parents has been added for the endpoint /rest/trait/all to the REST API v1.5 to return all the traits and the parents traits from the PGS Catalog database.
Best regards, Laurent
ramiromagno
commented
3 years ago Hi @ens-lgil ,
Did you mean include_children?
smlmbrt
commented
3 years ago The PGS that are associated with child traits from the ontology are listed in the child_associated_pgs_ids, whereas the PGS directly mapped to that EFO trait are included in the associated_pgs_ids list.
Previously only the EFO terms with directly associated scores were present in the endpoint (this would correspond to all child terms). The include_parents flag allows you to find the higher-level trait groupings from the EFO ontology that were only present in the search index before.
ramiromagno
commented
3 years ago okay, I see now.
Just to give you an idea of how I was representing the data prior to these changes:
include_children offAn object of class "traits"
Slot "traits":
# A tibble: 194 x 6
efo_id parent_efo_id is_child trait description url
<chr> <chr> <lgl> <chr> <chr> <chr>
1 EFO_0009… NA FALSE ACPA-negative rheum… "A subtype of rheumatoid arthritis defined by the absence of autoantibodies that are directed… http://www.ebi.ac.uk…
2 EFO_0009… NA FALSE ACPA-positive rheum… "A subtype of rheumatoid arthritis defined by the presence of autoantibodies that are directe… http://www.ebi.ac.uk…
3 EFO_0005… NA FALSE age at death "['The age at which death occurs.']" http://www.ebi.ac.uk…
4 EFO_0007… NA FALSE alcohol consumption… "['quantification of some aspect of alcohol consumption such as frequency or quantity']" http://www.ebi.ac.uk…
5 EFO_0007… NA FALSE alcohol dependence … "['quantification of some aspect of alcohol dependence or misuse, eg using a cummulative symp… http://www.ebi.ac.uk…
6 EFO_1000… NA FALSE alcoholic liver cir… "A disorder of the liver characterized by the presence of fibrotic scar tissue instead of hea… http://www.ebi.ac.uk…
7 EFO_0004… NA FALSE alkaline phosphatas… "['Alkaline phosphatase measurement is a quantification of alkaline phosphatase in blood. AP … http://www.ebi.ac.uk…
8 EFO_0000… NA FALSE Alzheimer's disease "A progressive, neurodegenerative disease characterized by loss of function and death of nerv… http://www.ebi.ac.uk…
9 EFO_0003… NA FALSE angina pectoris "['The symptom of paroxysmal pain consequent to MYOCARDIAL ISCHEMIA usually of distinctive ch… http://www.ebi.ac.uk…
10 EFO_0004… NA FALSE apolipoprotein A 1 … "['Is a quantification of serum lipoprotein A. Apolipoprotein A-I, encoded in humans by the A… http://www.ebi.ac.uk…
# … with 184 more rows
Slot "pgs_ids":
# A tibble: 761 x 4
efo_id parent_efo_id is_child pgs_id
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE PGS000195
2 EFO_0009459 NA FALSE PGS000194
3 EFO_0005056 NA FALSE PGS000318
4 EFO_0005056 NA FALSE PGS000319
5 EFO_0007878 NA FALSE PGS000203
6 EFO_0007878 NA FALSE PGS000204
7 EFO_0007835 NA FALSE PGS000201
8 EFO_0007835 NA FALSE PGS000202
9 EFO_1000802 NA FALSE PGS000704
10 EFO_0004533 NA FALSE PGS000670
# … with 751 more rows
Slot "child_pgs_ids":
# A tibble: 0 x 4
# … with 4 variables: efo_id <chr>, parent_efo_id <chr>, is_child <lgl>, child_pgs_id <chr>
Slot "trait_categories":
# A tibble: 227 x 4
efo_id parent_efo_id is_child trait_categories
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE Immune system disorder
2 EFO_0009459 NA FALSE Immune system disorder
3 EFO_0005056 NA FALSE Other measurement
4 EFO_0007878 NA FALSE Other measurement
5 EFO_0007835 NA FALSE Other measurement
6 EFO_1000802 NA FALSE Cancer
7 EFO_1000802 NA FALSE Digestive system disorder
8 EFO_0004533 NA FALSE Liver enzyme measurement
9 EFO_0000249 NA FALSE Neurological disorder
10 EFO_0003913 NA FALSE Other trait
# … with 217 more rows
Slot "trait_synonyms":
# A tibble: 2,005 x 4
efo_id parent_efo_id is_child trait_synonyms
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE anti-citrullinated protein antibody-negative rheumatoid arthritis
2 EFO_0009459 NA FALSE anti-citrullinated protein antibody-positive rheumatoid arthritis
3 EFO_0007835 NA FALSE alcohol misuse measurement
4 EFO_1000802 NA FALSE Alcoholic Cirrhosis
5 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver
6 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver (disorder)
7 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver (disorder) [Ambiguous]
8 EFO_1000802 NA FALSE Laennec's cirrhosis
9 EFO_1000802 NA FALSE Laennec's cirrhosis, alcoholic
10 EFO_1000802 NA FALSE Liver Cirrhosis, Alcoholic
# … with 1,995 more rows
Slot "trait_mapped_terms":
# A tibble: 1,326 x 4
efo_id parent_efo_id is_child trait_mapped_terms
<chr> <chr> <lgl> <chr>
1 EFO_0007878 NA FALSE PMID:26081443
2 EFO_0007835 NA FALSE PMID:27151647
3 EFO_1000802 NA FALSE COHD:196463
4 EFO_1000802 NA FALSE CSP:1754-7677
5 EFO_1000802 NA FALSE DOID:14018
6 EFO_1000802 NA FALSE ICD10:K70.3
7 EFO_1000802 NA FALSE ICD9:571.2
8 EFO_1000802 NA FALSE MESH:D008104
9 EFO_1000802 NA FALSE MONDO:0006644
10 EFO_1000802 NA FALSE MSH:D008104
# … with 1,316 more rowsinclude_children onAn object of class "traits"
Slot "traits":
# A tibble: 346 x 6
efo_id parent_efo_id is_child trait description url
<chr> <chr> <lgl> <chr> <chr> <chr>
1 EFO_0009… NA FALSE ACPA-negative rheumatoid … "A subtype of rheumatoid arthritis defined by the absence of autoantib… http://www.ebi.ac.uk/efo/EFO_0009460
2 EFO_0009… NA FALSE ACPA-positive rheumatoid … "A subtype of rheumatoid arthritis defined by the presence of autoanti… http://www.ebi.ac.uk/efo/EFO_0009459
3 EFO_0005… NA FALSE age at death "['The age at which death occurs.']" http://www.ebi.ac.uk/efo/EFO_0005056
4 EFO_0007… NA FALSE alcohol consumption measu… "['quantification of some aspect of alcohol consumption such as freque… http://www.ebi.ac.uk/efo/EFO_0007878
5 EFO_0007… NA FALSE alcohol dependence measur… "['quantification of some aspect of alcohol dependence or misuse, eg u… http://www.ebi.ac.uk/efo/EFO_0007835
6 EFO_1000… NA FALSE alcoholic liver cirrhosis "A disorder of the liver characterized by the presence of fibrotic sca… http://www.ebi.ac.uk/efo/EFO_1000802
7 EFO_0004… NA FALSE alkaline phosphatase meas… "['Alkaline phosphatase measurement is a quantification of alkaline ph… http://www.ebi.ac.uk/efo/EFO_0004533
8 EFO_0000… NA FALSE Alzheimer's disease "A progressive, neurodegenerative disease characterized by loss of fun… http://www.ebi.ac.uk/efo/EFO_0000249
9 EFO_1001… EFO_0000249 TRUE late-onset Alzheimers dis… "['This is the most common form of the disease, which happens to peopl… http://www.ebi.ac.uk/efo/EFO_1001870
10 EFO_0003… NA FALSE angina pectoris "['The symptom of paroxysmal pain consequent to MYOCARDIAL ISCHEMIA us… http://www.ebi.ac.uk/efo/EFO_0003913
11 EFO_0004… NA FALSE apolipoprotein A 1 measur… "['Is a quantification of serum lipoprotein A. Apolipoprotein A-I, enc… http://www.ebi.ac.uk/efo/EFO_0004614
12 EFO_0004… NA FALSE apolipoprotein B measurem… "['The measurement of ApoB in blood. Apolipoprotein B is a major prote… http://www.ebi.ac.uk/efo/EFO_0004615
13 EFO_0004… NA FALSE aspartate aminotransferas… "['Is a quantification of aspartate aminotransferase, and is commonly … http://www.ebi.ac.uk/efo/EFO_0004736
14 EFO_0010… NA FALSE aspartate aminotransferas… "['The ratio between the levels of aspartate aminotransferase (AST) an… http://www.ebi.ac.uk/efo/EFO_0010934
15 EFO_0000… NA FALSE asthma "A bronchial disease that is characterized by chronic inflammation and… http://www.ebi.ac.uk/efo/EFO_0000270
16 EFO_0000… NA FALSE atrial fibrillation "A disorder characterized by an electrocardiographic finding of a supr… http://www.ebi.ac.uk/efo/EFO_0000275
17 EFO_0003… NA FALSE autism spectrum disorder "A spectrum of developmental disorders that includes autism, and Asper… http://www.ebi.ac.uk/efo/EFO_0003756
18 EFO_0000… NA FALSE Barrett's esophagus "Esophageal lesion lined with columnar metaplastic epithelium which is… http://www.ebi.ac.uk/efo/EFO_0000280
19 EFO_0004… NA FALSE basal cell carcinoma "A carcinoma involving the basal cells. [NCIT: C156767]" http://www.ebi.ac.uk/efo/EFO_0004193
20 EFO_0005… NA FALSE basophil count "['quantification of basophils in the blood', 'The number of granulocy… http://www.ebi.ac.uk/efo/EFO_0005090
21 EFO_0007… EFO_0005090 TRUE basophil percentage of le… "['A calculated measurement in which the number of basophil granulocyt… http://www.ebi.ac.uk/efo/EFO_0007992
22 EFO_0007… NA FALSE basophil percentage of le… "['A calculated measurement in which the number of basophil granulocyt… http://www.ebi.ac.uk/efo/EFO_0007992
23 EFO_0004… NA FALSE bilirubin measurement "['A bilirubin measurement is a quantification of bilirubin typically … http://www.ebi.ac.uk/efo/EFO_0004570
24 EFO_0000… NA FALSE bladder carcinoma "A carcinoma that arises from epithelial cells of the urinary bladder … http://www.ebi.ac.uk/efo/EFO_0000292
25 EFO_0007… NA FALSE blood protein measurement "['quantification of the levels of some protein in a blood sample']" http://www.ebi.ac.uk/efo/EFO_0007937
26 EFO_0008… NA FALSE BMI-adjusted fasting bloo… "fasting blood glucose measurement that has been adjusted for subjects… http://www.ebi.ac.uk/efo/EFO_0008036
27 EFO_0008… NA FALSE BMI-adjusted fasting bloo… "fasting insulin measurement that has been adjusted for subjects' body… http://www.ebi.ac.uk/efo/EFO_0008037
28 EFO_0007… NA FALSE BMI-adjusted waist-hip ra… "['waist-hip ratio that has been adjusted by subjects’ body mass index… http://www.ebi.ac.uk/efo/EFO_0007788
29 EFO_0004… NA FALSE body height "['The distance from the sole to the crown of the head with body stand… http://www.ebi.ac.uk/efo/EFO_0004339
30 EFO_0004… NA FALSE body mass index "['An indicator of body density as determined by the relationship of B… http://www.ebi.ac.uk/efo/EFO_0004340
31 EFO_0003… NA FALSE bone density "['The amount of mineral per square centimeter of BONE. This is the de… http://www.ebi.ac.uk/efo/EFO_0003923
32 MONDO_00… NA FALSE brain cancer "A primary or metastatic malignant neoplasm affecting the brain. [NCIT… http://purl.obolibrary.org/obo/MONDO_…
33 EFO_0000… NA FALSE breast carcinoma "A carcinoma that arises from epithelial cells of the breast [MONDO: D… http://www.ebi.ac.uk/efo/EFO_0000305
34 EFO_1000… EFO_0000305 TRUE estrogen-receptor negativ… "A subtype of breast cancer that is estrogen-receptor negative [EFO: 1… http://www.ebi.ac.uk/efo/EFO_1000650
35 MONDO_00… EFO_0000305 TRUE luminal A breast carcinoma "A biologic subset of breast carcinoma defined by high expression of g… http://purl.obolibrary.org/obo/MONDO_…
36 MONDO_00… EFO_0000305 TRUE luminal B breast carcinoma "A biologic subset of breast carcinoma defined by low to moderate expr… http://purl.obolibrary.org/obo/MONDO_…
37 EFO_1000… EFO_0000305 TRUE estrogen-receptor positiv… "A subtype of breast cancer that is estrogen-receptor positive [EFO: 1… http://www.ebi.ac.uk/efo/EFO_1000649
38 EFO_1000… EFO_0000305 TRUE HER2 Positive Breast Carc… "A biologic subset of breast carcinoma defined by high expression of H… http://www.ebi.ac.uk/efo/EFO_1000294
39 MONDO_00… EFO_0000305 TRUE Her2-receptor negative br… NA https://www.ebi.ac.uk/ols/ontologies/…
40 EFO_0005… EFO_0000305 TRUE triple-negative breast ca… "An invasive breast carcinoma which is negative for expression of estr… http://www.ebi.ac.uk/efo/EFO_0005537
41 MONDO_00… NA FALSE bronchus cancer "A malignant neoplasm involving the bronchus [MONDO: DesignPattern]" http://purl.obolibrary.org/obo/MONDO_…
42 EFO_0007… NA FALSE calcaneal bone quantitati… "['bone quantitiave ultrasound of the main bone in the heel, recognize… http://www.ebi.ac.uk/efo/EFO_0007772
43 EFO_0004… NA FALSE calcium measurement "['Is a quantification of calcium, typically in serum. Calcium (Ca2+) … http://www.ebi.ac.uk/efo/EFO_0004838
44 EFO_0000… NA FALSE cancer "A tumor composed of atypical neoplastic, often pleomorphic cells that… http://www.ebi.ac.uk/efo/EFO_0000311
45 EFO_0001… EFO_0000311 TRUE cervical carcinoma "A carcinoma arising from either the exocervical squamous epithelium o… http://www.ebi.ac.uk/efo/EFO_0001061
46 EFO_0000… EFO_0000311 TRUE cutaneous melanoma "A primary melanoma arising from atypical melanocytes in the skin. Pre… http://www.ebi.ac.uk/efo/EFO_0000389
47 EFO_0000… EFO_0000311 TRUE melanoma "A malignant, usually aggressive tumor composed of atypical, neoplasti… http://www.ebi.ac.uk/efo/EFO_0000756
48 EFO_0005… EFO_0000311 TRUE colorectal cancer "A primary or metastatic malignant neoplasm that affects the colon or … http://www.ebi.ac.uk/efo/EFO_0005842
49 EFO_0001… EFO_0000311 TRUE multiple myeloma "A bone marrow-based plasma cell neoplasm characterized by a serum mon… http://www.ebi.ac.uk/efo/EFO_0001378
50 EFO_0002… EFO_0000311 TRUE thyroid carcinoma "A carcinoma arising from the thyroid gland. It is usually an adenocar… http://www.ebi.ac.uk/efo/EFO_0002892
# … with 296 more rows
Slot "pgs_ids":
# A tibble: 1,560 x 4
efo_id parent_efo_id is_child pgs_id
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE PGS000195
2 EFO_0009459 NA FALSE PGS000194
3 EFO_0005056 NA FALSE PGS000318
4 EFO_0005056 NA FALSE PGS000319
5 EFO_0007878 NA FALSE PGS000203
6 EFO_0007878 NA FALSE PGS000204
7 EFO_0007835 NA FALSE PGS000201
8 EFO_0007835 NA FALSE PGS000202
9 EFO_1000802 NA FALSE PGS000704
10 EFO_0004533 NA FALSE PGS000670
11 EFO_0000249 NA FALSE PGS000025
12 EFO_0000249 NA FALSE PGS000026
13 EFO_1001870 EFO_0000249 TRUE PGS000053
14 EFO_1001870 EFO_0000249 TRUE PGS000054
15 EFO_1001870 EFO_0000249 TRUE PGS000334
16 EFO_0003913 NA FALSE PGS000703
17 EFO_0004614 NA FALSE PGS000671
18 EFO_0004615 NA FALSE PGS000672
19 EFO_0004736 NA FALSE PGS000673
20 EFO_0010934 NA FALSE PGS000674
21 EFO_0000270 NA FALSE PGS000037
22 EFO_0000275 NA FALSE PGS000016
23 EFO_0000275 NA FALSE PGS000035
24 EFO_0000275 NA FALSE PGS000331
25 EFO_0000275 NA FALSE PGS000338
26 EFO_0003756 NA FALSE PGS000327
27 EFO_0000280 NA FALSE PGS000085
28 EFO_0004193 NA FALSE PGS000119
29 EFO_0004193 NA FALSE PGS000445
30 EFO_0004193 NA FALSE PGS000446
31 EFO_0004193 NA FALSE PGS000447
32 EFO_0004193 NA FALSE PGS000448
33 EFO_0004193 NA FALSE PGS000449
34 EFO_0004193 NA FALSE PGS000450
35 EFO_0004193 NA FALSE PGS000451
36 EFO_0004193 NA FALSE PGS000452
37 EFO_0004193 NA FALSE PGS000453
38 EFO_0004193 NA FALSE PGS000454
39 EFO_0004193 NA FALSE PGS000455
40 EFO_0004193 NA FALSE PGS000456
41 EFO_0004193 NA FALSE PGS000457
42 EFO_0004193 NA FALSE PGS000458
43 EFO_0004193 NA FALSE PGS000459
44 EFO_0005090 NA FALSE PGS000088
45 EFO_0005090 NA FALSE PGS000163
46 EFO_0007992 EFO_0005090 TRUE PGS000089
47 EFO_0007992 EFO_0005090 TRUE PGS000164
48 EFO_0007992 NA FALSE PGS000089
49 EFO_0007992 NA FALSE PGS000164
50 EFO_0004570 NA FALSE PGS000681
# … with 1,510 more rows
Slot "child_pgs_ids":
# A tibble: 1,157 x 4
efo_id parent_efo_id is_child child_pgs_id
<chr> <chr> <lgl> <chr>
1 EFO_0000249 NA FALSE PGS000053
2 EFO_0000249 NA FALSE PGS000054
3 EFO_0000249 NA FALSE PGS000334
4 EFO_0005090 NA FALSE PGS000089
5 EFO_0005090 NA FALSE PGS000164
6 EFO_0000305 NA FALSE PGS000002
7 EFO_0000305 NA FALSE PGS000003
8 EFO_0000305 NA FALSE PGS000005
9 EFO_0000305 NA FALSE PGS000006
10 EFO_0000305 NA FALSE PGS000008
11 EFO_0000305 NA FALSE PGS000009
12 EFO_0000305 NA FALSE PGS000046
13 EFO_0000305 NA FALSE PGS000047
14 EFO_0000305 NA FALSE PGS000212
15 EFO_0000305 NA FALSE PGS000213
16 EFO_0000305 NA FALSE PGS000214
17 EFO_0000305 NA FALSE PGS000215
18 EFO_0000305 NA FALSE PGS000216
19 EFO_0000305 NA FALSE PGS000346
20 EFO_0000305 NA FALSE PGS000347
21 EFO_1000650 EFO_0000305 TRUE PGS000216
22 MONDO_0000618 EFO_0000305 TRUE PGS000216
23 EFO_0000311 NA FALSE PGS000001
24 EFO_0000311 NA FALSE PGS000002
25 EFO_0000311 NA FALSE PGS000003
26 EFO_0000311 NA FALSE PGS000004
27 EFO_0000311 NA FALSE PGS000005
28 EFO_0000311 NA FALSE PGS000006
29 EFO_0000311 NA FALSE PGS000007
30 EFO_0000311 NA FALSE PGS000008
31 EFO_0000311 NA FALSE PGS000009
32 EFO_0000311 NA FALSE PGS000015
33 EFO_0000311 NA FALSE PGS000028
34 EFO_0000311 NA FALSE PGS000029
35 EFO_0000311 NA FALSE PGS000030
36 EFO_0000311 NA FALSE PGS000044
37 EFO_0000311 NA FALSE PGS000045
38 EFO_0000311 NA FALSE PGS000046
39 EFO_0000311 NA FALSE PGS000047
40 EFO_0000311 NA FALSE PGS000048
41 EFO_0000311 NA FALSE PGS000049
42 EFO_0000311 NA FALSE PGS000050
43 EFO_0000311 NA FALSE PGS000051
44 EFO_0000311 NA FALSE PGS000052
45 EFO_0000311 NA FALSE PGS000055
46 EFO_0000311 NA FALSE PGS000067
47 EFO_0000311 NA FALSE PGS000068
48 EFO_0000311 NA FALSE PGS000069
49 EFO_0000311 NA FALSE PGS000070
50 EFO_0000311 NA FALSE PGS000071
# … with 1,107 more rows
Slot "trait_categories":
# A tibble: 406 x 4
efo_id parent_efo_id is_child trait_categories
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE Immune system disorder
2 EFO_0009459 NA FALSE Immune system disorder
3 EFO_0005056 NA FALSE Other measurement
4 EFO_0007878 NA FALSE Other measurement
5 EFO_0007835 NA FALSE Other measurement
6 EFO_1000802 NA FALSE Cancer
7 EFO_1000802 NA FALSE Digestive system disorder
8 EFO_0004533 NA FALSE Liver enzyme measurement
9 EFO_0000249 NA FALSE Neurological disorder
10 EFO_1001870 EFO_0000249 TRUE Neurological disorder
11 EFO_0003913 NA FALSE Other trait
12 EFO_0004614 NA FALSE Cardiovascular measurement
13 EFO_0004614 NA FALSE Inflammatory measurement
14 EFO_0004614 NA FALSE Lipid or lipoprotein measurement
15 EFO_0004615 NA FALSE Lipid or lipoprotein measurement
16 EFO_0004736 NA FALSE Liver enzyme measurement
17 EFO_0010934 NA FALSE Other measurement
18 EFO_0000270 NA FALSE Other disease
19 EFO_0000275 NA FALSE Cardiovascular disease
20 EFO_0003756 NA FALSE Neurological disorder
21 EFO_0000280 NA FALSE Digestive system disorder
22 EFO_0004193 NA FALSE Cancer
23 EFO_0005090 NA FALSE Hematological measurement
24 EFO_0005090 NA FALSE Inflammatory measurement
25 EFO_0007992 EFO_0005090 TRUE Hematological measurement
26 EFO_0007992 EFO_0005090 TRUE Inflammatory measurement
27 EFO_0007992 NA FALSE Hematological measurement
28 EFO_0007992 NA FALSE Inflammatory measurement
29 EFO_0004570 NA FALSE Other measurement
30 EFO_0000292 NA FALSE Cancer
31 EFO_0007937 NA FALSE Other measurement
32 EFO_0008036 NA FALSE Other measurement
33 EFO_0008037 NA FALSE Other measurement
34 EFO_0007788 NA FALSE Body measurement
35 EFO_0004339 NA FALSE Body measurement
36 EFO_0004340 NA FALSE Body measurement
37 EFO_0003923 NA FALSE Other measurement
38 MONDO_0001657 NA FALSE Cancer
39 MONDO_0001657 NA FALSE Neurological disorder
40 EFO_0000305 NA FALSE Cancer
41 EFO_1000650 EFO_0000305 TRUE Cancer
42 MONDO_0021116 EFO_0000305 TRUE Cancer
43 MONDO_0021115 EFO_0000305 TRUE Cancer
44 EFO_1000649 EFO_0000305 TRUE Cancer
45 EFO_1000294 EFO_0000305 TRUE Cancer
46 MONDO_0000618 EFO_0000305 TRUE Cancer
47 EFO_0005537 EFO_0000305 TRUE Cancer
48 MONDO_0001672 NA FALSE Cancer
49 EFO_0007772 NA FALSE Other measurement
50 EFO_0004838 NA FALSE Other measurement
# … with 356 more rows
Slot "trait_synonyms":
# A tibble: 4,313 x 4
efo_id parent_efo_id is_child trait_synonyms
<chr> <chr> <lgl> <chr>
1 EFO_0009460 NA FALSE anti-citrullinated protein antibody-negative rheumatoid arthritis
2 EFO_0009459 NA FALSE anti-citrullinated protein antibody-positive rheumatoid arthritis
3 EFO_0007835 NA FALSE alcohol misuse measurement
4 EFO_1000802 NA FALSE Alcoholic Cirrhosis
5 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver
6 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver (disorder)
7 EFO_1000802 NA FALSE Alcoholic cirrhosis of liver (disorder) [Ambiguous]
8 EFO_1000802 NA FALSE Laennec's cirrhosis
9 EFO_1000802 NA FALSE Laennec's cirrhosis, alcoholic
10 EFO_1000802 NA FALSE Liver Cirrhosis, Alcoholic
11 EFO_1000802 NA FALSE Portal Cirrhosis
12 EFO_1000802 NA FALSE Portal cirrhosis
13 EFO_1000802 NA FALSE Portal cirrhosis (disorder)
14 EFO_1000802 NA FALSE Portal cirrhosis unspecified (disorder)
15 EFO_1000802 NA FALSE alcoholic cirrhosis
16 EFO_1000802 NA FALSE alcoholic cirrhosis of liver
17 EFO_1000802 NA FALSE alcoholic liver cirrhosis
18 EFO_1000802 NA FALSE portal cirrhosis
19 EFO_0004533 NA FALSE AP
20 EFO_0000249 NA FALSE AD
21 EFO_0000249 NA FALSE AD - Alzheimer's disease
22 EFO_0000249 NA FALSE ALZHEIMER DIS
23 EFO_0000249 NA FALSE ALZHEIMERS DIS
24 EFO_0000249 NA FALSE Alzheimer Dementia
25 EFO_0000249 NA FALSE Alzheimer Dementia, Presenile
26 EFO_0000249 NA FALSE Alzheimer Disease
27 EFO_0000249 NA FALSE Alzheimer Type Dementia
28 EFO_0000249 NA FALSE Alzheimer dementia
29 EFO_0000249 NA FALSE Alzheimer disease
30 EFO_0000249 NA FALSE Alzheimer's
31 EFO_0000249 NA FALSE Alzheimer's Dementia
32 EFO_0000249 NA FALSE Alzheimer's dementia
33 EFO_0000249 NA FALSE Alzheimer's disease
34 EFO_0000249 NA FALSE Alzheimer's disease (disorder)
35 EFO_0000249 NA FALSE Alzheimer's disease, NOS
36 EFO_0000249 NA FALSE Alzheimers
37 EFO_0000249 NA FALSE Alzheimers Dementia
38 EFO_0000249 NA FALSE Alzheimers dementia
39 EFO_0000249 NA FALSE Alzheimers disease
40 EFO_0000249 NA FALSE DAT - Dementia Alzheimer's type
41 EFO_0000249 NA FALSE Dementia in Alzheimer's disease
42 EFO_0000249 NA FALSE Dementia in Alzheimer's disease (disorder)
43 EFO_0000249 NA FALSE Dementia in Alzheimer's disease, unspecified (disorder)
44 EFO_0000249 NA FALSE Dementia of the Alzheimer's type
45 EFO_0000249 NA FALSE Dementia, Alzheimer Type
46 EFO_0000249 NA FALSE Dementia, Presenile
47 EFO_0000249 NA FALSE Dementia, Presenile Alzheimer
48 EFO_0000249 NA FALSE Disease, Alzheimer
49 EFO_0000249 NA FALSE Disease, Alzheimer's
50 EFO_0000249 NA FALSE Presenile Alzheimer Dementia
# … with 4,263 more rows
Slot "trait_mapped_terms":
# A tibble: 2,717 x 4
efo_id parent_efo_id is_child trait_mapped_terms
<chr> <chr> <lgl> <chr>
1 EFO_0007878 NA FALSE PMID:26081443
2 EFO_0007835 NA FALSE PMID:27151647
3 EFO_1000802 NA FALSE COHD:196463
4 EFO_1000802 NA FALSE CSP:1754-7677
5 EFO_1000802 NA FALSE DOID:14018
6 EFO_1000802 NA FALSE ICD10:K70.3
7 EFO_1000802 NA FALSE ICD9:571.2
8 EFO_1000802 NA FALSE MESH:D008104
9 EFO_1000802 NA FALSE MONDO:0006644
10 EFO_1000802 NA FALSE MSH:D008104
11 EFO_1000802 NA FALSE MedDRA:10001618
12 EFO_1000802 NA FALSE NCIT:C34782
13 EFO_1000802 NA FALSE NCIt:C34782
14 EFO_1000802 NA FALSE SCTID:419728003
15 EFO_1000802 NA FALSE SNOMEDCT:420054005
16 EFO_1000802 NA FALSE UMLS:C0023891
17 EFO_1000802 NA FALSE UMLS:C1622502
18 EFO_0004533 NA FALSE NCIt:C64432
19 EFO_0004533 NA FALSE SNOMEDCT:88810008
20 EFO_0000249 NA FALSE COHD:378419
21 EFO_0000249 NA FALSE DOID:10652
22 EFO_0000249 NA FALSE GARD:0000632
23 EFO_0000249 NA FALSE HP:0002511
24 EFO_0000249 NA FALSE ICD10:G30
25 EFO_0000249 NA FALSE ICD10:G30.9
26 EFO_0000249 NA FALSE ICD9:290.1
27 EFO_0000249 NA FALSE ICD9:331.0
28 EFO_0000249 NA FALSE KEGG:05010
29 EFO_0000249 NA FALSE MESH:D000544
30 EFO_0000249 NA FALSE MONDO:0004975
31 EFO_0000249 NA FALSE MSH:D000544
32 EFO_0000249 NA FALSE NCIT:C2866
33 EFO_0000249 NA FALSE NCIt:C2866
34 EFO_0000249 NA FALSE NCIt:C34524
35 EFO_0000249 NA FALSE NCIt:C38778
36 EFO_0000249 NA FALSE NIFSTD:birnlex_2092
37 EFO_0000249 NA FALSE OMIM:104300
38 EFO_0000249 NA FALSE OMIM:502500
39 EFO_0000249 NA FALSE OMIM:605526
40 EFO_0000249 NA FALSE OMIM:608907
41 EFO_0000249 NA FALSE OMIM:615590
42 EFO_0000249 NA FALSE OMIM:615711
43 EFO_0000249 NA FALSE SCTID:142811000119104
44 EFO_0000249 NA FALSE SNOMEDCT:12348006
45 EFO_0000249 NA FALSE SNOMEDCT:15662003
46 EFO_0000249 NA FALSE SNOMEDCT:26929004
47 EFO_0000249 NA FALSE UMLS:C0002395
48 EFO_0003913 NA FALSE ICD10:I20
49 EFO_0003913 NA FALSE ICD9:413
50 EFO_0003913 NA FALSE MSH:D000787
# … with 2,667 more rows
It would be nice to provide the parameter
include_childrento the/rest/trait/allendpoint.Right now what I do, as an alternative, is to get all EFO identifiers with
/rest/trait/allfirst, and then run one request to/rest/trait/{trait_id}for each EFO identifier; not ideal.