Skip to content

Commit 488d030

Browse files
sigvensigven
committed
EFO 3.71, DO Sept 2024 release
1 parent 2093ae7 commit 488d030

File tree

11 files changed

+646
-10
lines changed

11 files changed

+646
-10
lines changed

‎R/sysdata.rda‎

10 Bytes
Binary file not shown.

‎README.md‎

Lines changed: 8 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -30,21 +30,24 @@ is possible.
3030
In short, **phenOncoX** provides a global cross-mapped set of phenotype
3131
ontology terms attributed to cancer phenotypes.
3232

33-
The mapping established within **phenOncoX** is semi-manually curated, using [OncoTree](http://oncotree.mskcc.org/#/home) as the starting point for a list of [UMLS](https://www.ncbi.nlm.nih.gov/medgen/) phenotype terms per cancer
33+
The mapping established within **phenOncoX** is semi-manually curated,
34+
using [OncoTree](http://oncotree.mskcc.org/#/home) as the starting point
35+
for a list of [UMLS](https://www.ncbi.nlm.nih.gov/medgen/) phenotype terms per cancer
3436
subtype/primary site. Next, **phenOncoX** appends a number of phenotypes
3537
attributed to heritable cancer conditions. Furthermore, each cancer subtype
3638
entry in *OncoTree* is expanded with additional subtypes that are found in
3739
the *UMLS* child-parent hierarchy of disease terms.
3840

3941
For each entry in the final list of phenotype terms, we make cross-mappings
4042
with phenotype terms from [EFO](https://github.com/EBISPOT/efo),
41-
[DO](https://disease-ontology.org/), and the [ICD10 classification](https://www.who.int/standards/classifications/classification-of-diseases).
43+
[DO](https://disease-ontology.org/), and
44+
the [ICD10 classification](https://www.who.int/standards/classifications/classification-of-diseases).
4245

43-
As of early September 2024, the following ontology versions are used to create the mapping:
46+
As of late October 2024, the following ontology versions are used to create the mapping:
4447

4548
- OncoTree (2021_11_02)
46-
- Experimental Factor Ontology v3.69.0 (2024-08-15)
47-
- Disease Ontology (v2024-08-28)
49+
- Experimental Factor Ontology v3.71.0 (2024-10-15)
50+
- Disease Ontology (v2024-09-27)
4851

4952
**IMPORTANT NOTE**: The mapping established by **phenOncoX** attempts
5053
to be comprehensive, but we acknowledge that the presence of missing or

‎data-raw/data-raw.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -73,7 +73,7 @@ db[['oncotree_core']] <- oncotree_core
7373
db[['oncotree_expanded']] <- oncotree_expanded
7474
db[['auxiliary_maps']] <- auxiliary_maps
7575

76-
version_bumped <- "0.7.9"
76+
version_bumped <- "0.8.0"
7777
gd_records <- list()
7878
db_id_ref <- data.frame()
7979

‎data-raw/fimm_icd10/Disease.2024-05-14_20_06_08.tsv‎

Lines changed: 202 additions & 0 deletions
Large diffs are not rendered by default.

‎data-raw/fimm_icd10/fimm_icd10.tsv‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
Disease.2024-05-14_20_06_08.tsv

‎data-raw/fimm_icd10/fimm_icd10_pcgr_20240618.tsv‎

Lines changed: 137 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,137 @@
1+
reference_database icd10_code name tumor_site_pcgr
2+
ICD-10 C00 Malignant neoplasm of lip Head and Neck
3+
ICD-10 C01 Malignant neoplasm of base of tongue Head and Neck
4+
ICD-10 C02 Malignant neoplasm of other and unspecified parts of tongue Head and Neck
5+
ICD-10 C03 Malignant neoplasm of gum Head and Neck
6+
ICD-10 C04 Malignant neoplasm of floor of mouth Head and Neck
7+
ICD-10 C05 Malignant neoplasm of palate Head and Neck
8+
ICD-10 C06 Malignant neoplasm of other and unspecified parts of mouth Head and Neck
9+
ICD-10 C07 Malignant neoplasm of parotid gland Head and Neck
10+
ICD-10 C08 Malignant neoplasm of other and unspecified major salivary glands Head and Neck
11+
ICD-10 C09 Malignant neoplasm of tonsil Head and Neck
12+
ICD-10 C10 Malignant neoplasm of oropharynx Head and Neck
13+
ICD-10 C11 Malignant neoplasm of nasopharynx Head and Neck
14+
ICD-10 C12 Malignant neoplasm of pyriform sinus Head and Neck
15+
ICD-10 C13 Malignant neoplasm of hypopharynx Head and Neck
16+
ICD-10 C14 Malignant neoplasm of other and ill-defined sites in the lip, oral cavity and pharynx Head and Neck
17+
ICD-10 C15 Malignant neoplasm of oesophagus Esophagus/Stomach
18+
ICD-10 C16 Malignant neoplasm of stomach Esophagus/Stomach
19+
ICD-10 C17 Malignant neoplasm of small intestine Esophagus/Stomach
20+
ICD-10 C18 Malignant neoplasm of colon Colon/Rectum
21+
ICD-10 C19 Malignant neoplasm of rectosigmoid junction Colon/Rectum
22+
ICD-10 C20 Malignant neoplasm of rectum Colon/Rectum
23+
ICD-10 C21 Malignant neoplasm of anus and anal canal Colon/Rectum
24+
ICD-10 C22 Malignant neoplasm of liver and intrahepatic bile ducts Biliary Tract;Liver
25+
ICD-10 C23 Malignant neoplasm of gallbladder Biliary Tract
26+
ICD-10 C24 Malignant neoplasm of other and unspecified parts of biliary tract Biliary Tract
27+
ICD-10 C25 Malignant neoplasm of pancreas Pancreas
28+
ICD-10 C26 Malignant neoplasm of other and ill-defined digestive organs Esophagus/Stomach
29+
ICD-10 C30 Malignant neoplasm of nasal cavity and middle ear Head and Neck
30+
ICD-10 C31 Malignant neoplasm of accessory sinuses Head and Neck
31+
ICD-10 C32 Malignant neoplasm of larynx Head and Neck
32+
ICD-10 C33 Malignant neoplasm of trachea Lung
33+
ICD-10 C34 Malignant neoplasm of bronchus and lung Lung
34+
ICD-10 C37 Malignant neoplasm of thymus Thymus
35+
ICD-10 C38 Malignant neoplasm of heart, mediastinum and pleura NA
36+
ICD-10 C39 Malignant neoplasm of other and ill-defined sites in the respiratory system and intrathoracic organs Lung
37+
ICD-10 C40 Malignant neoplasm of bone and articular cartilage of limbs Bone
38+
ICD-10 C41 Malignant neoplasm of bone and articular cartilage of other and unspecified sites Bone
39+
ICD-10 C43 Malignant melanoma of skin Skin
40+
ICD-10 C44 Other malignant neoplasms of skin Skin
41+
ICD-10 C45 Mesothelioma Pleura
42+
ICD-10 C46 Kaposi's sarcoma Skin;Soft Tissue
43+
ICD-10 C47 Malignant neoplasm of peripheral nerves and autonomic nervous system Peripheral Nervous System
44+
ICD-10 C48 Malignant neoplasm of retroperitoneum and peritoneum Peritoneum
45+
ICD-10 C49 Malignant neoplasm of other connective and soft tissue Soft Tissue
46+
ICD-10 C50 Malignant neoplasm of breast Breast
47+
ICD-10 C51 Malignant neoplasm of vulva Vulva/Vagina
48+
ICD-10 C52 Malignant neoplasm of vagina Vulva/Vagina
49+
ICD-10 C53 Malignant neoplasm of cervix uteri Cervix
50+
ICD-10 C54 Malignant neoplasm of corpus uteri Uterus
51+
ICD-10 C55 Malignant neoplasm of uterus, part unspecified Bladder/Urinary Tract
52+
ICD-10 C56 Malignant neoplasm of ovary Ovary/Fallopian Tube
53+
ICD-10 C57 Malignant neoplasm of other and unspecified female genital organs Ovary/Fallopian Tube
54+
ICD-10 C58 Malignant neoplasm of placenta Uterus
55+
ICD-10 C60 Malignant neoplasm of penis Penis
56+
ICD-10 C61 Malignant neoplasm of prostate Prostate
57+
ICD-10 C62 Malignant neoplasm of testis Testis
58+
ICD-10 C63 Malignant neoplasm of other and unspecified male genital organs Testis
59+
ICD-10 C64 Malignant neoplasm of kidney, except renal pelvis Kidney
60+
ICD-10 C65 Malignant neoplasm of renal pelvis Bladder/Urinary Tract
61+
ICD-10 C66 Malignant neoplasm of ureter Bladder/Urinary Tract
62+
ICD-10 C67 Malignant neoplasm of bladder Bladder/Urinary Tract
63+
ICD-10 C68 Malignant neoplasm of other and unspecified urinary organs Bladder/Urinary Tract
64+
ICD-10 C69 Malignant neoplasm of eye and adnexa Eye
65+
ICD-10 C70 Malignant neoplasm of meninges CNS/Brain
66+
ICD-10 C71 Malignant neoplasm of brain CNS/Brain
67+
ICD-10 C72 Malignant neoplasm of spinal cord, cranial nerves and other parts of central nervous system CNS/Brain
68+
ICD-10 C73 Malignant neoplasm of thyroid gland Thyroid
69+
ICD-10 C74 Malignant neoplasm of adrenal gland Adrenal Gland
70+
ICD-10 C75 Malignant neoplasm of other endocrine glands and related structures CNS/Brain
71+
ICD-10 C76 Malignant neoplasm of other and ill-defined sites Lung
72+
ICD-10 C77 Secondary and unspecified malignant neoplasm of lymph nodes NA
73+
ICD-10 C78 Secondary malignant neoplasm of respiratory and digestive organs Esophagus/Stomach;Lung
74+
ICD-10 C79 Secondary malignant neoplasm of other sites NA
75+
ICD-10 C80 Malignant neoplasm without specification of site NA
76+
ICD-10 C81 Hodgkin's disease Lymphoid
77+
ICD-10 C82 Follicular [nodular] non-Hodgkin's lymphoma Lymphoid
78+
ICD-10 C83 Diffuse non-Hodgkin's lymphoma Lymphoid
79+
ICD-10 C84 Peripheral and cutaneous T-cell lymphomas Lymphoid
80+
ICD-10 C85 Other and unspecified types of non-Hodgkin's lymphoma Lymphoid
81+
ICD-10 C88 Malignant immunoproliferative diseases Lymphoid
82+
ICD-10 C90 Multiple myeloma and malignant plasma cell neoplasms Lymphoid;Myeloid
83+
ICD-10 C91 Lymphoid leukaemia Myeloid
84+
ICD-10 C92 Myeloid leukaemia Myeloid
85+
ICD-10 C93 Monocytic leukaemia Myeloid
86+
ICD-10 C94 Other leukaemias of specified cell type Myeloid
87+
ICD-10 C95 Leukaemia of unspecified cell type Myeloid
88+
ICD-10 C96 Other and unspecified malignant neoplasms of lymphoid, haematopoietic and related tissue Lymphoid;Myeloid
89+
ICD-10 C97 Malignant neoplasms of independent (primary) multiple sites NA
90+
ICD-10 D00 Carcinoma in situ of oral cavity, oesophagus and stomach Esophagus/Stomach
91+
ICD-10 D01 Carcinoma in situ of other and unspecified digestive organs Esophagus/Stomach
92+
ICD-10 D02 Carcinoma in situ of middle ear and respiratory system Head and Neck
93+
ICD-10 D03 Melanoma in situ Skin
94+
ICD-10 D04 Carcinoma in situ of skin Skin
95+
ICD-10 D05 Carcinoma in situ of breast Breast
96+
ICD-10 D06 Carcinoma in situ of cervix uteri Cervix
97+
ICD-10 D07 Carcinoma in situ of other and unspecified genital organs Prostate
98+
ICD-10 D09 Carcinoma in situ of other and unspecified sites Bladder/Urinary Tract
99+
ICD-10 D10 Benign neoplasm of mouth and pharynx Head and Neck
100+
ICD-10 D11 Benign neoplasm of major salivary glands NA
101+
ICD-10 D12 Benign neoplasm of colon, rectum, anus and anal canal Colon/Rectum
102+
ICD-10 D13 Benign neoplasm of other and ill-defined parts of digestive system Esophagus/Stomach
103+
ICD-10 D14 Benign neoplasm of middle ear and respiratory system Head and Neck
104+
ICD-10 D15 Benign neoplasm of other and unspecified intrathoracic organs Lung
105+
ICD-10 D16 Benign neoplasm of bone and articular cartilage Bone
106+
ICD-10 D17 Benign lipomatous neoplasm Soft Tissue
107+
ICD-10 D18 Haemangioma and lymphangioma, any site Soft Tissue
108+
ICD-10 D19 Benign neoplasm of mesothelial tissue Pleura
109+
ICD-10 D20 Benign neoplasm of soft tissue of retroperitoneum and peritoneum Peritoneum;Soft Tissue
110+
ICD-10 D21 Other benign neoplasms of connective and other soft tissue Soft Tissue
111+
ICD-10 D22 Melanocytic naevi Skin
112+
ICD-10 D23 Other benign neoplasms of skin Skin
113+
ICD-10 D24 Benign neoplasm of breast Breast
114+
ICD-10 D25 Leiomyoma of uterus Soft Tissue;Uterus
115+
ICD-10 D26 Other benign neoplasms of uterus Uterus
116+
ICD-10 D27 Benign neoplasm of ovary Ovary/Fallopian Tube
117+
ICD-10 D28 Benign neoplasm of other and unspecified female genital organs NA
118+
ICD-10 D29 Benign neoplasm of male genital organs NA
119+
ICD-10 D30 Benign neoplasm of urinary organs NA
120+
ICD-10 D31 Benign neoplasm of eye and adnexa Eye
121+
ICD-10 D32 Benign neoplasm of meninges CNS/Brain
122+
ICD-10 D33 Benign neoplasm of brain and other parts of central nervous system CNS/Brain
123+
ICD-10 D34 Benign neoplasm of thyroid gland Thyroid
124+
ICD-10 D35 Benign neoplasm of other and unspecified endocrine glands NA
125+
ICD-10 D36 Benign neoplasm of other and unspecified sites NA
126+
ICD-10 D37 Neoplasm of uncertain or unknown behaviour of oral cavity and digestive organs Esophagus/Stomach
127+
ICD-10 D38 Neoplasm of uncertain or unknown behaviour of middle ear and respiratory and intrathoracic organs Head and Neck
128+
ICD-10 D39 Neoplasm of uncertain or unknown behaviour of female genital organs NA
129+
ICD-10 D40 Neoplasm of uncertain or unknown behaviour of male genital organs NA
130+
ICD-10 D41 Neoplasm of uncertain or unknown behaviour of urinary organs Bladder/Urinary Tract
131+
ICD-10 D42 Neoplasm of uncertain or unknown behaviour of meninges CNS/Brain
132+
ICD-10 D43 Neoplasm of uncertain or unknown behaviour of brain and central nervous system CNS/Brain
133+
ICD-10 D44 Neoplasm of uncertain or unknown behaviour of endocrine glands NA
134+
ICD-10 D45 Polycythaemia vera Myeloid
135+
ICD-10 D46 Myelodysplastic syndromes Lymphoid;Myeloid
136+
ICD-10 D47 Other neoplasms of uncertain or unknown behaviour of lymphoid, haematopoietic and related tissue Myeloid
137+
ICD-10 D48 Neoplasm of uncertain or unknown behaviour of other and unspecified sites NA

0 commit comments

Comments
 (0)