Exploration of MAxO
The Medical Action Ontology (MAxO) (https://obofoundry.org/ontology/maxo) is an ontology of medical procedures, interventions, therapies, and treatments for disease with an emphasis on rare disease (RD).
This notebooks shows an exploration of the contents of MAxO. It focuses on the ontology content, but as annotations are added we will include these.
Setup
We will use the sqlite version of MAxO. In this notebook we will set up an alias for convenience.
Note on the command line the syntax is different, for unix systems:
alias maxo="runoak -i sqlite:obo:maxo"
[21]:
%alias maxo runoak -i sqlite:obo:maxo
Let’s start by getting some basic metadata about the ontology.
NOTE the first time you run this there may be a lag while the pre-made sqlite database for maxo is downloaded
[4]:
maxo ontology-metadata --all
dce:creator:
- Leigh Carmody
- Peter Robinson
dce:description:
- An ontology to represent medically relevant actions, procedures, therapies, interventions,
and recommendations.
dce:title:
- Medical Action Ontology
dcterms:license:
- <https://creativecommons.org/licenses/by/4.0/>
id:
- obo:maxo.owl
owl:versionIRI:
- obo:maxo/releases/2022-12-19/maxo.owl
owl:versionInfo:
- '2022-12-19'
rdf:type:
- owl:Ontology
rdfs:isDefinedBy:
- http://purl.obolibrary.org/obo/obo.owl
schema:url:
- http://purl.obolibrary.org/obo/maxo.owl
sh:prefix:
- obo
Root terms
We will query for roots (all terms without an is-a parent)
This reveals a few dangling classes that should be cleared up
[5]:
maxo roots -p i
id label
BFO:0000001 entity
CARO:0000003 None
CARO:0000006 None
CARO:0001001 None
CARO:0001010 None
CARO:0010000 None
CL:0000000 cell
CL:0017500 neutrophillic cytoplasm
CL:0017502 acidophilic cytoplasm
CL:0017503 basophilic cytoplasm
CL:0017504 polychromatophilic cytoplasm
CL:0017505 increased nucleus size
HP:0000001 All
MAXO:0000001 medical action
NCBITaxon:110815 None
NCBITaxon:147099 None
NCBITaxon:147554 None
NCBITaxon:189497 None
NCBITaxon:3176 None
NCBITaxon:3312 None
NCBITaxon:33630 None
NCBITaxon:33682 None
NCBITaxon:3378 None
NCBITaxon:38254 None
NCBITaxon:4891 None
NCBITaxon:4895 None
NCBITaxon:4896 None
NCBITaxon:4932 None
NCBITaxon:5782 None
NCBITaxon:Union_0000023 None
SO:0000110 sequence_feature
Roots in the MAXO id space
As can be seen above there is a single root node in the MAXO namespace
We can also query for MAXO-roots, i.e classes in MAXO that have no MAXO is-a parent:
[7]:
maxo roots -p i --has-prefix MAXO
Visualization
We can use the viz command to see the full ancestry for any term or set of terms or term query.
For now, we will restrict to is-a parents (-p i):
[5]:
maxo viz -p i 'biopsy of thymus' 'biopsy of thyroid gland' -o output/maxo-biopsy.png
TODO: add explanation of why BFO processes show up
Upper level
We can use the tree command to explore the upper level:
[8]:
maxo tree -p i MAXO:0000001 MAXO:0000058 MAXO:0000002 MAXO:0000003 MAXO:0000013 MAXO:0000017 MAXO:0000021 MAXO:0001014
* [] **MAXO:0000001 ! medical action**
* [i] **MAXO:0000002 ! therapeutic procedure**
* [i] **MAXO:0000058 ! pharmacotherapy**
* [i] **MAXO:0000003 ! diagnostic procedure**
* [i] **MAXO:0000013 ! complementary and alternative medical therapy**
* [i] **MAXO:0000017 ! preventative therapeutics**
* [i] **MAXO:0000021 ! palliative care**
* [i] **MAXO:0001014 ! medical action avoidance**
Summary Statistics
We can get summary statistics using the statistics command.
Note that like many ontologies, MAXO comes “bundled” with other ontologies, so it’s important to pass in --has-prefix to restrict summary statistics only to things in the MAXO space.
[22]:
maxo statistics --has-prefix MAXO > output/maxo-stats.yaml
This generates a YAML object (download from output/maxo-stats.yaml).
let’s take a look at the output. It’s quite large so we’ll use the unix head command:
[23]:
!head -25 output/maxo-stats.yaml
annotation_property_count: 0
class_count: 1440
class_count_with_text_definitions: 1374
class_count_without_text_definitions: 66
contributor_summary:
<http://orcid.org/0000-0001-7941-2961>:
contributor_id: <http://orcid.org/0000-0001-7941-2961>
role_counts:
oio:created_by:
facet: oio:created_by
filtered_count: 822
<http://orcid.org/0000-0002-7463-6306>:
contributor_id: <http://orcid.org/0000-0002-7463-6306>
role_counts:
oio:created_by:
facet: oio:created_by
filtered_count: 3
http://orcid.org/0000-0001-7941-2961:
contributor_id: http://orcid.org/0000-0001-7941-2961
contributor_name: http://orcid.org/0000-0001-7941-2961
role_counts:
oio:created_by:
facet: oio:created_by
filtered_count: 491
http://orcid.org/0000-0001-7941-29610:
Note that the main stats are buried further down.
You can get the same thing in JSON. There is a cached copy you can view on https://jsonblob.com/1069350711447535616
[24]:
maxo statistics --has-prefix MAXO -O json > output/maxo-stats.json
The YAML and JSON view is best for seeing the more complete granular results, but for many purposes a tabular view is better.
We can do that with -O csv (the -O is short for --output-type, which is available for more OAK commands)
[25]:
maxo statistics --has-prefix MAXO -O csv -o output/maxo-stats.tsv
Download: output/maxo-stats.tsv
You can then browse the output using whatever method you prefer, e.g. load into excel.
In a Jupyter notebook, pandas dataframes are a convenient way to explore tabular data:
[32]:
import pandas as pd
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', None)
[33]:
df = pd.read_csv("output/maxo-stats.tsv", sep="\t").fillna("")
df
[33]:
| id | compared_with | agents | class_count | deprecated_class_count | non_deprecated_class_count | class_count_with_text_definitions | class_count_without_text_definitions | object_property_count | annotation_property_count | named_individual_count | subset_count | rdf_triple_count | subclass_of_axiom_count | equivalent_classes_axiom_count | entailed_edge_count_by_predicate | distinct_synonym_count | synonym_statement_count | class_count_by_category | contributor_summary | change_summary | merged_class_query | deprecated_property_count | edge_count_by_predicate_BFO:0000051 | edge_count_by_predicate_MAXO:0000521 | edge_count_by_predicate_MAXO:0000864 | edge_count_by_predicate_MAXO:0001015 | edge_count_by_predicate_MAXO:0001027 | edge_count_by_predicate_RO:0002233 | edge_count_by_predicate_rdfs:subClassOf | synonym_statement_count_by_predicate_hasBroadSynonym | synonym_statement_count_by_predicate_hasExactSynonym | synonym_statement_count_by_predicate_hasNarrowSynonym | synonym_statement_count_by_predicate_hasRelatedSynonym | mapping_statement_count_by_predicate_hasDbXref | mapping_statement_count_by_object_source_OGMS | mapping_statement_count_by_object_source_NCIT | mapping_statement_count_by_object_source_OAE | mapping_statement_count_by_object_source_SIO | mapping_statement_count_by_object_source_ERO | mapping_statement_count_by_object_source_NCRO | mapping_statement_count_by_object_source_SCDO | mapping_statement_count_by_object_source_OMIT | mapping_statement_count_by_object_source_CHEBI | mapping_statement_count_by_object_source_MeSH | mapping_statement_count_by_object_source_OBI | mapping_statement_count_by_object_source_IDO | mapping_statement_count_by_object_source_VO | mapping_statement_count_by_object_source_https | mapping_statement_count_by_object_source_PMID | mapping_statement_count_by_object_source_NCIt | mapping_statement_count_by_object_source_UMLS_CUI | mapping_statement_count_by_object_source_CMO | mapping_statement_count_by_object_source_NCBIBook | mapping_statement_count_by_object_source_MMO | mapping_statement_count_by_object_source_VSO | mapping_statement_count_by_object_source_http | mapping_statement_count_by_object_source_EFO | mapping_statement_count_by_object_source_IDOMAL | mapping_statement_count_subject_by_object_source_OGMS | mapping_statement_count_subject_by_object_source_NCIT | mapping_statement_count_subject_by_object_source_OAE | mapping_statement_count_subject_by_object_source_SIO | mapping_statement_count_subject_by_object_source_ERO | mapping_statement_count_subject_by_object_source_NCRO | mapping_statement_count_subject_by_object_source_SCDO | mapping_statement_count_subject_by_object_source_OMIT | mapping_statement_count_subject_by_object_source_CHEBI | mapping_statement_count_subject_by_object_source_MeSH | mapping_statement_count_subject_by_object_source_OBI | mapping_statement_count_subject_by_object_source_IDO | mapping_statement_count_subject_by_object_source_VO | mapping_statement_count_subject_by_object_source_https | mapping_statement_count_subject_by_object_source_PMID | mapping_statement_count_subject_by_object_source_NCIt | mapping_statement_count_subject_by_object_source_UMLS_CUI | mapping_statement_count_subject_by_object_source_CMO | mapping_statement_count_subject_by_object_source_NCBIBook | mapping_statement_count_subject_by_object_source_MMO | mapping_statement_count_subject_by_object_source_VSO | mapping_statement_count_subject_by_object_source_http | mapping_statement_count_subject_by_object_source_EFO | mapping_statement_count_subject_by_object_source_IDOMAL | was_generated_by_started_at_time | was_generated_by_was_associated_with | was_generated_by_acted_on_behalf_of | ontologies_id | ontologies_version | ontologies_version_info | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | AllOntologies | [] | [] | 1440 | 53 | 1387 | 1374 | 66 | 4 | 0 | 0 | 0 | 15642 | 2842 | 584 | {} | 4391 | 4391 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 8 | 20 | 134 | 9 | 76 | 441 | 2154 | 25 | 4250 | 97 | 19 | 554 | 8 | 330 | 2 | 1 | 4 | 2 | 5 | 5 | 134 | 20 | 15 | 1 | 4 | 3 | 11 | 1 | 1 | 6 | 5 | 1 | 4 | 2 | 1 | 1 | 8 | 321 | 2 | 1 | 4 | 2 | 5 | 5 | 133 | 20 | 15 | 1 | 4 | 3 | 11 | 1 | 1 | 6 | 5 | 1 | 4 | 2 | 1 | 1 | 2023-01-29T12:44:00.348450 | OAK | cjm | obo:maxo.owl | obo:maxo/releases/2022-12-19/maxo.owl | 2022-12-19 |
the default TSV output for most OAK commands follows a TidyData format, with one row per item.
Let’s unpivot this for easy viewing, using pandas melt:
[34]:
df.melt()
[34]:
| variable | value | |
|---|---|---|
| 0 | id | AllOntologies |
| 1 | compared_with | [] |
| 2 | agents | [] |
| 3 | class_count | 1440 |
| 4 | deprecated_class_count | 53 |
| 5 | non_deprecated_class_count | 1387 |
| 6 | class_count_with_text_definitions | 1374 |
| 7 | class_count_without_text_definitions | 66 |
| 8 | object_property_count | 4 |
| 9 | annotation_property_count | 0 |
| 10 | named_individual_count | 0 |
| 11 | subset_count | 0 |
| 12 | rdf_triple_count | 15642 |
| 13 | subclass_of_axiom_count | 2842 |
| 14 | equivalent_classes_axiom_count | 584 |
| 15 | entailed_edge_count_by_predicate | {} |
| 16 | distinct_synonym_count | 4391 |
| 17 | synonym_statement_count | 4391 |
| 18 | class_count_by_category | {} |
| 19 | contributor_summary | {'http://orcid.org/0000-0001-7941-2961': Contr... |
| 20 | change_summary | {} |
| 21 | merged_class_query | 0 |
| 22 | deprecated_property_count | 0 |
| 23 | edge_count_by_predicate_BFO:0000051 | 8 |
| 24 | edge_count_by_predicate_MAXO:0000521 | 20 |
| 25 | edge_count_by_predicate_MAXO:0000864 | 134 |
| 26 | edge_count_by_predicate_MAXO:0001015 | 9 |
| 27 | edge_count_by_predicate_MAXO:0001027 | 76 |
| 28 | edge_count_by_predicate_RO:0002233 | 441 |
| 29 | edge_count_by_predicate_rdfs:subClassOf | 2154 |
| 30 | synonym_statement_count_by_predicate_hasBroadS... | 25 |
| 31 | synonym_statement_count_by_predicate_hasExactS... | 4250 |
| 32 | synonym_statement_count_by_predicate_hasNarrow... | 97 |
| 33 | synonym_statement_count_by_predicate_hasRelate... | 19 |
| 34 | mapping_statement_count_by_predicate_hasDbXref | 554 |
| 35 | mapping_statement_count_by_object_source_OGMS | 8 |
| 36 | mapping_statement_count_by_object_source_NCIT | 330 |
| 37 | mapping_statement_count_by_object_source_OAE | 2 |
| 38 | mapping_statement_count_by_object_source_SIO | 1 |
| 39 | mapping_statement_count_by_object_source_ERO | 4 |
| 40 | mapping_statement_count_by_object_source_NCRO | 2 |
| 41 | mapping_statement_count_by_object_source_SCDO | 5 |
| 42 | mapping_statement_count_by_object_source_OMIT | 5 |
| 43 | mapping_statement_count_by_object_source_CHEBI | 134 |
| 44 | mapping_statement_count_by_object_source_MeSH | 20 |
| 45 | mapping_statement_count_by_object_source_OBI | 15 |
| 46 | mapping_statement_count_by_object_source_IDO | 1 |
| 47 | mapping_statement_count_by_object_source_VO | 4 |
| 48 | mapping_statement_count_by_object_source_https | 3 |
| 49 | mapping_statement_count_by_object_source_PMID | 11 |
| 50 | mapping_statement_count_by_object_source_NCIt | 1 |
| 51 | mapping_statement_count_by_object_source_UMLS_CUI | 1 |
| 52 | mapping_statement_count_by_object_source_CMO | 6 |
| 53 | mapping_statement_count_by_object_source_NCBIBook | 5 |
| 54 | mapping_statement_count_by_object_source_MMO | 1 |
| 55 | mapping_statement_count_by_object_source_VSO | 4 |
| 56 | mapping_statement_count_by_object_source_http | 2 |
| 57 | mapping_statement_count_by_object_source_EFO | 1 |
| 58 | mapping_statement_count_by_object_source_IDOMAL | 1 |
| 59 | mapping_statement_count_subject_by_object_sour... | 8 |
| 60 | mapping_statement_count_subject_by_object_sour... | 321 |
| 61 | mapping_statement_count_subject_by_object_sour... | 2 |
| 62 | mapping_statement_count_subject_by_object_sour... | 1 |
| 63 | mapping_statement_count_subject_by_object_sour... | 4 |
| 64 | mapping_statement_count_subject_by_object_sour... | 2 |
| 65 | mapping_statement_count_subject_by_object_sour... | 5 |
| 66 | mapping_statement_count_subject_by_object_sour... | 5 |
| 67 | mapping_statement_count_subject_by_object_sour... | 133 |
| 68 | mapping_statement_count_subject_by_object_sour... | 20 |
| 69 | mapping_statement_count_subject_by_object_sour... | 15 |
| 70 | mapping_statement_count_subject_by_object_sour... | 1 |
| 71 | mapping_statement_count_subject_by_object_sour... | 4 |
| 72 | mapping_statement_count_subject_by_object_sour... | 3 |
| 73 | mapping_statement_count_subject_by_object_sour... | 11 |
| 74 | mapping_statement_count_subject_by_object_sour... | 1 |
| 75 | mapping_statement_count_subject_by_object_sour... | 1 |
| 76 | mapping_statement_count_subject_by_object_sour... | 6 |
| 77 | mapping_statement_count_subject_by_object_sour... | 5 |
| 78 | mapping_statement_count_subject_by_object_sour... | 1 |
| 79 | mapping_statement_count_subject_by_object_sour... | 4 |
| 80 | mapping_statement_count_subject_by_object_sour... | 2 |
| 81 | mapping_statement_count_subject_by_object_sour... | 1 |
| 82 | mapping_statement_count_subject_by_object_sour... | 1 |
| 83 | was_generated_by_started_at_time | 2023-01-29T12:44:00.348450 |
| 84 | was_generated_by_was_associated_with | OAK |
| 85 | was_generated_by_acted_on_behalf_of | cjm |
| 86 | ontologies_id | obo:maxo.owl |
| 87 | ontologies_version | obo:maxo/releases/2022-12-19/maxo.owl |
| 88 | ontologies_version_info | 2022-12-19 |
Note that the original YAML report included many “nested” summaries, where counts were broken down by a facet - e.g. edge counts:
edge_count_by_predicate:
BFO:0000051:
facet: BFO:0000051
filtered_count: 8
MAXO:0000521:
facet: MAXO:0000521
filtered_count: 20
MAXO:0000864:
facet: MAXO:0000864
filtered_count: 134
...
These get flattened (“denormalized”) in the conversion to TSV, creating a new column for each facet, but this isn’t done for all objects since this would make too wide a table (e.g. the contributor report, some ontologies may have 100s of contributors).
E.g.
variable |
value |
|---|---|
edge_count_by_predicate_BFO:0000051 |
8 |
edge_count_by_predicate_MAXO:0000521 |
20 |
edge_count_by_predicate_MAXO:0000864 |
134 |
The fields names may be verbose but they are intended to be unambiguous. One problem with ontology stats reporting is that there is often built in ambiguity; e.g what does “number of terms” mean?
number of classes
number of classes plus relations (object properties?)
are obsolete classes included? what about merged classes?
If you want to look up documentation for any of these fields, just prefix with https://incatools.github.io/ontology-access-kit/datamodels/summary-statistics/
(in future these elements may have their own w3id URIs)
Note this only works for “non-denormalized” fields - to interpret “edge_count_by_predicate_BFO:0000051” you must split this into the base statistic edge_count_by_predicate and the entity (BFO:0000051, aka has-part). Or you can simply look at the native normalized YAML output.
Summarizing by branches
We can pass in a list of branches:
[29]:
maxo statistics --has-prefix MAXO -O csv -o output/maxo-stats-roots.tsv MAXO:0000001 MAXO:0000058 MAXO:0000002 MAXO:0000003 MAXO:0000013 MAXO:0000017 MAXO:0000021 MAXO:0001014
You can download this: output/maxo-stats-roots.tsv and use excel etc to view.
Or see this google sheet
[37]:
df = pd.read_csv("output/maxo-stats-roots.tsv", sep="\t").fillna("")
df
[37]:
| id | compared_with | agents | class_count | deprecated_class_count | non_deprecated_class_count | class_count_with_text_definitions | class_count_without_text_definitions | object_property_count | annotation_property_count | named_individual_count | subset_count | rdf_triple_count | subclass_of_axiom_count | equivalent_classes_axiom_count | entailed_edge_count_by_predicate | distinct_synonym_count | synonym_statement_count | class_count_by_category | contributor_summary | change_summary | merged_class_query | deprecated_property_count | edge_count_by_predicate_BFO:0000051 | edge_count_by_predicate_MAXO:0000521 | edge_count_by_predicate_MAXO:0000864 | edge_count_by_predicate_MAXO:0001015 | edge_count_by_predicate_MAXO:0001027 | edge_count_by_predicate_RO:0002233 | edge_count_by_predicate_rdfs:subClassOf | synonym_statement_count_by_predicate_hasBroadSynonym | synonym_statement_count_by_predicate_hasExactSynonym | synonym_statement_count_by_predicate_hasNarrowSynonym | synonym_statement_count_by_predicate_hasRelatedSynonym | mapping_statement_count_by_predicate_hasDbXref | mapping_statement_count_by_object_source_OGMS | mapping_statement_count_by_object_source_NCIT | mapping_statement_count_by_object_source_OAE | mapping_statement_count_by_object_source_SIO | mapping_statement_count_by_object_source_ERO | mapping_statement_count_by_object_source_NCRO | mapping_statement_count_by_object_source_SCDO | mapping_statement_count_by_object_source_OMIT | mapping_statement_count_by_object_source_CHEBI | mapping_statement_count_by_object_source_MeSH | mapping_statement_count_by_object_source_OBI | mapping_statement_count_by_object_source_IDO | mapping_statement_count_by_object_source_VO | mapping_statement_count_by_object_source_https | mapping_statement_count_by_object_source_PMID | mapping_statement_count_by_object_source_NCIt | mapping_statement_count_by_object_source_UMLS_CUI | mapping_statement_count_by_object_source_CMO | mapping_statement_count_by_object_source_NCBIBook | mapping_statement_count_by_object_source_MMO | mapping_statement_count_by_object_source_VSO | mapping_statement_count_by_object_source_http | mapping_statement_count_by_object_source_EFO | mapping_statement_count_by_object_source_IDOMAL | mapping_statement_count_subject_by_object_source_OGMS | mapping_statement_count_subject_by_object_source_NCIT | mapping_statement_count_subject_by_object_source_OAE | mapping_statement_count_subject_by_object_source_SIO | mapping_statement_count_subject_by_object_source_ERO | mapping_statement_count_subject_by_object_source_NCRO | mapping_statement_count_subject_by_object_source_SCDO | mapping_statement_count_subject_by_object_source_OMIT | mapping_statement_count_subject_by_object_source_CHEBI | mapping_statement_count_subject_by_object_source_MeSH | mapping_statement_count_subject_by_object_source_OBI | mapping_statement_count_subject_by_object_source_IDO | mapping_statement_count_subject_by_object_source_VO | mapping_statement_count_subject_by_object_source_https | mapping_statement_count_subject_by_object_source_PMID | mapping_statement_count_subject_by_object_source_NCIt | mapping_statement_count_subject_by_object_source_UMLS_CUI | mapping_statement_count_subject_by_object_source_CMO | mapping_statement_count_subject_by_object_source_NCBIBook | mapping_statement_count_subject_by_object_source_MMO | mapping_statement_count_subject_by_object_source_VSO | mapping_statement_count_subject_by_object_source_http | mapping_statement_count_subject_by_object_source_EFO | mapping_statement_count_subject_by_object_source_IDOMAL | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | medical action | [] | [] | 1387 | 0 | 1387 | 1374 | 13 | 0 | 0 | 0 | 0 | 15355 | 2789 | 584 | {} | 4385 | 4385 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 8.0 | 20.0 | 134.0 | 9.0 | 76.0 | 441.0 | 2101 | 25.0 | 4246 | 97.0 | 17.0 | 553.0 | 8.0 | 329.0 | 2.0 | 1.0 | 4.0 | 2.0 | 5.0 | 5.0 | 134.0 | 19.0 | 15.0 | 1.0 | 4.0 | 3.0 | 11.0 | 1.0 | 1.0 | 6.0 | 5.0 | 1.0 | 4.0 | 2.0 | 1.0 | 1.0 | 8.0 | 320.0 | 2.0 | 1.0 | 4.0 | 2.0 | 5.0 | 5.0 | 133.0 | 19.0 | 15.0 | 1.0 | 4.0 | 3.0 | 11.0 | 1.0 | 1.0 | 6.0 | 5.0 | 1.0 | 4.0 | 2.0 | 1.0 | 1.0 |
| 1 | pharmacotherapy | [] | [] | 256 | 0 | 256 | 248 | 8 | 0 | 0 | 0 | 0 | 3772 | 556 | 134 | {} | 1553 | 1553 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 134.0 | 422 | 12.0 | 1515 | 19.0 | 7.0 | 196.0 | 1.0 | 57.0 | 1.0 | 1.0 | 134.0 | 2.0 | 1.0 | 1.0 | 56.0 | 1.0 | 1.0 | 133.0 | 2.0 | 1.0 | |||||||||||||||||||||||||||||||||||||||
| 2 | therapeutic procedure | [] | [] | 898 | 0 | 898 | 885 | 13 | 0 | 0 | 0 | 0 | 10555 | 1853 | 394 | {} | 3363 | 3363 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 9.0 | 134.0 | 76.0 | 260.0 | 1374 | 24.0 | 3262 | 65.0 | 12.0 | 386.0 | 6.0 | 203.0 | 2.0 | 1.0 | 4.0 | 2.0 | 3.0 | 4.0 | 134.0 | 19.0 | 1.0 | 3.0 | 6.0 | 1.0 | 1.0 | 2.0 | 2.0 | 6.0 | 195.0 | 2.0 | 1.0 | 4.0 | 2.0 | 3.0 | 4.0 | 133.0 | 19.0 | 1.0 | 3.0 | 6.0 | 1.0 | 1.0 | 2.0 | 2.0 | ||||||||||||||||
| 3 | diagnostic procedure | [] | [] | 556 | 0 | 556 | 556 | 0 | 0 | 0 | 0 | 0 | 5888 | 1140 | 254 | {} | 1492 | 1492 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 8.0 | 246.0 | 886 | 2.0 | 1452 | 32.0 | 6.0 | 180.0 | 1.0 | 151.0 | 1.0 | 12.0 | 5.0 | 6.0 | 3.0 | 1.0 | 4.0 | 1.0 | 150.0 | 1.0 | 12.0 | 5.0 | 6.0 | 3.0 | 1.0 | 4.0 | ||||||||||||||||||||||||||||||||||
| 4 | complementary and alternative medical therapy | [] | [] | 6 | 0 | 6 | 6 | 0 | 0 | 0 | 0 | 0 | 53 | 6 | 0 | {} | 9 | 9 | {} | {'<http://orcid.org/0000-0001-7941-2961>': Con... | {} | 0 | 0 | 6 | 7 | 2.0 | 8.0 | 6.0 | 2.0 | 6.0 | 2.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 5 | preventative therapeutics | [] | [] | 22 | 0 | 22 | 22 | 0 | 0 | 0 | 0 | 0 | 206 | 34 | 1 | {} | 46 | 46 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 11.0 | 23 | 46 | 14.0 | 6.0 | 2.0 | 1.0 | 4.0 | 1.0 | 1.0 | 6.0 | 2.0 | 1.0 | 4.0 | 1.0 | 1.0 | ||||||||||||||||||||||||||||||||||||||||||||
| 6 | palliative care | [] | [] | 6 | 0 | 6 | 6 | 0 | 0 | 0 | 0 | 0 | 59 | 8 | 0 | {} | 15 | 15 | {} | {'<http://orcid.org/0000-0001-7941-2961>': Con... | {} | 0 | 0 | 8 | 7 | 8.0 | 6.0 | 5.0 | 1.0 | 4.0 | 1.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||
| 7 | medical action avoidance | [] | [] | 9 | 0 | 9 | 9 | 0 | 0 | 0 | 0 | 0 | 81 | 18 | 0 | {} | 18 | 18 | {} | {'http://orcid.org/0000-0001-7941-2961': Contr... | {} | 0 | 0 | 9.0 | 9 | 18 |
Here each row is a branch (note that numbers are cumulative, so numbers for a parent include numbers for children, even if there is a separate row for that child).
Note that you will never see deprecated classes when using this option, if the deprecated classes are not in the hierarchy (as is conventional for OBO ontologies)
We may prefer to view the transposed form:
[38]:
df.convert_dtypes().transpose()
[38]:
| 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | |
|---|---|---|---|---|---|---|---|---|
| id | medical action | pharmacotherapy | therapeutic procedure | diagnostic procedure | complementary and alternative medical therapy | preventative therapeutics | palliative care | medical action avoidance |
| compared_with | [] | [] | [] | [] | [] | [] | [] | [] |
| agents | [] | [] | [] | [] | [] | [] | [] | [] |
| class_count | 1387 | 256 | 898 | 556 | 6 | 22 | 6 | 9 |
| deprecated_class_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| non_deprecated_class_count | 1387 | 256 | 898 | 556 | 6 | 22 | 6 | 9 |
| class_count_with_text_definitions | 1374 | 248 | 885 | 556 | 6 | 22 | 6 | 9 |
| class_count_without_text_definitions | 13 | 8 | 13 | 0 | 0 | 0 | 0 | 0 |
| object_property_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| annotation_property_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| named_individual_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| subset_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| rdf_triple_count | 15355 | 3772 | 10555 | 5888 | 53 | 206 | 59 | 81 |
| subclass_of_axiom_count | 2789 | 556 | 1853 | 1140 | 6 | 34 | 8 | 18 |
| equivalent_classes_axiom_count | 584 | 134 | 394 | 254 | 0 | 1 | 0 | 0 |
| entailed_edge_count_by_predicate | {} | {} | {} | {} | {} | {} | {} | {} |
| distinct_synonym_count | 4385 | 1553 | 3363 | 1492 | 9 | 46 | 15 | 18 |
| synonym_statement_count | 4385 | 1553 | 3363 | 1492 | 9 | 46 | 15 | 18 |
| class_count_by_category | {} | {} | {} | {} | {} | {} | {} | {} |
| contributor_summary | {'http://orcid.org/0000-0001-7941-2961': Contr... | {'http://orcid.org/0000-0001-7941-2961': Contr... | {'http://orcid.org/0000-0001-7941-2961': Contr... | {'http://orcid.org/0000-0001-7941-2961': Contr... | {'<http://orcid.org/0000-0001-7941-2961>': Con... | {'http://orcid.org/0000-0001-7941-2961': Contr... | {'<http://orcid.org/0000-0001-7941-2961>': Con... | {'http://orcid.org/0000-0001-7941-2961': Contr... |
| change_summary | {} | {} | {} | {} | {} | {} | {} | {} |
| merged_class_query | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| deprecated_property_count | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| edge_count_by_predicate_BFO:0000051 | 8.0 | 8.0 | ||||||
| edge_count_by_predicate_MAXO:0000521 | 20.0 | 9.0 | 11.0 | |||||
| edge_count_by_predicate_MAXO:0000864 | 134.0 | 134.0 | 134.0 | |||||
| edge_count_by_predicate_MAXO:0001015 | 9.0 | 9.0 | ||||||
| edge_count_by_predicate_MAXO:0001027 | 76.0 | 76.0 | ||||||
| edge_count_by_predicate_RO:0002233 | 441.0 | 260.0 | 246.0 | |||||
| edge_count_by_predicate_rdfs:subClassOf | 2101 | 422 | 1374 | 886 | 6 | 23 | 8 | 9 |
| synonym_statement_count_by_predicate_hasBroadSynonym | 25.0 | 12.0 | 24.0 | 2.0 | ||||
| synonym_statement_count_by_predicate_hasExactSynonym | 4246 | 1515 | 3262 | 1452 | 7 | 46 | 7 | 18 |
| synonym_statement_count_by_predicate_hasNarrowSynonym | 97.0 | 19.0 | 65.0 | 32.0 | 2.0 | 8.0 | ||
| synonym_statement_count_by_predicate_hasRelatedSynonym | 17.0 | 7.0 | 12.0 | 6.0 | ||||
| mapping_statement_count_by_predicate_hasDbXref | 553.0 | 196.0 | 386.0 | 180.0 | 8.0 | 14.0 | 6.0 | |
| mapping_statement_count_by_object_source_OGMS | 8.0 | 1.0 | 6.0 | 1.0 | ||||
| mapping_statement_count_by_object_source_NCIT | 329.0 | 57.0 | 203.0 | 151.0 | 6.0 | 6.0 | 5.0 | |
| mapping_statement_count_by_object_source_OAE | 2.0 | 2.0 | ||||||
| mapping_statement_count_by_object_source_SIO | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_ERO | 4.0 | 4.0 | 1.0 | |||||
| mapping_statement_count_by_object_source_NCRO | 2.0 | 1.0 | 2.0 | |||||
| mapping_statement_count_by_object_source_SCDO | 5.0 | 3.0 | 2.0 | |||||
| mapping_statement_count_by_object_source_OMIT | 5.0 | 1.0 | 4.0 | 1.0 | ||||
| mapping_statement_count_by_object_source_CHEBI | 134.0 | 134.0 | 134.0 | |||||
| mapping_statement_count_by_object_source_MeSH | 19.0 | 19.0 | ||||||
| mapping_statement_count_by_object_source_OBI | 15.0 | 1.0 | 12.0 | 2.0 | ||||
| mapping_statement_count_by_object_source_IDO | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_VO | 4.0 | 4.0 | ||||||
| mapping_statement_count_by_object_source_https | 3.0 | 2.0 | 3.0 | |||||
| mapping_statement_count_by_object_source_PMID | 11.0 | 1.0 | 6.0 | 5.0 | ||||
| mapping_statement_count_by_object_source_NCIt | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_UMLS_CUI | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_CMO | 6.0 | 6.0 | ||||||
| mapping_statement_count_by_object_source_NCBIBook | 5.0 | 2.0 | 3.0 | |||||
| mapping_statement_count_by_object_source_MMO | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_VSO | 4.0 | 4.0 | ||||||
| mapping_statement_count_by_object_source_http | 2.0 | 2.0 | ||||||
| mapping_statement_count_by_object_source_EFO | 1.0 | 1.0 | ||||||
| mapping_statement_count_by_object_source_IDOMAL | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_OGMS | 8.0 | 1.0 | 6.0 | 1.0 | ||||
| mapping_statement_count_subject_by_object_source_NCIT | 320.0 | 56.0 | 195.0 | 150.0 | 6.0 | 6.0 | 4.0 | |
| mapping_statement_count_subject_by_object_source_OAE | 2.0 | 2.0 | ||||||
| mapping_statement_count_subject_by_object_source_SIO | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_ERO | 4.0 | 4.0 | 1.0 | |||||
| mapping_statement_count_subject_by_object_source_NCRO | 2.0 | 1.0 | 2.0 | |||||
| mapping_statement_count_subject_by_object_source_SCDO | 5.0 | 3.0 | 2.0 | |||||
| mapping_statement_count_subject_by_object_source_OMIT | 5.0 | 1.0 | 4.0 | 1.0 | ||||
| mapping_statement_count_subject_by_object_source_CHEBI | 133.0 | 133.0 | 133.0 | |||||
| mapping_statement_count_subject_by_object_source_MeSH | 19.0 | 19.0 | ||||||
| mapping_statement_count_subject_by_object_source_OBI | 15.0 | 1.0 | 12.0 | 2.0 | ||||
| mapping_statement_count_subject_by_object_source_IDO | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_VO | 4.0 | 4.0 | ||||||
| mapping_statement_count_subject_by_object_source_https | 3.0 | 2.0 | 3.0 | |||||
| mapping_statement_count_subject_by_object_source_PMID | 11.0 | 1.0 | 6.0 | 5.0 | ||||
| mapping_statement_count_subject_by_object_source_NCIt | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_UMLS_CUI | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_CMO | 6.0 | 6.0 | ||||||
| mapping_statement_count_subject_by_object_source_NCBIBook | 5.0 | 2.0 | 3.0 | |||||
| mapping_statement_count_subject_by_object_source_MMO | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_VSO | 4.0 | 4.0 | ||||||
| mapping_statement_count_subject_by_object_source_http | 2.0 | 2.0 | ||||||
| mapping_statement_count_subject_by_object_source_EFO | 1.0 | 1.0 | ||||||
| mapping_statement_count_subject_by_object_source_IDOMAL | 1.0 | 1.0 |
Note that the categories are not disjoint - some terms can be in more than one branch, and “medical action” covers everything.
Exploring mappings
Next let’s use OAK to query mappings in MAXO. There are a lot, so for exploration purposes let’s fetch this for all terms that have the string “biopsy” in them:
[39]:
maxo mappings l~biopsy -O sssom
# curie_map: {}
# license: UNSPECIFIED
# mapping_set_id: temp
subject_id subject_label predicate_id object_id object_label mapping_justification subject_source object_source
MAXO:0000332 biopsy of anus oio:hasDbXref NCIT:C51586 semapv:UnspecifiedMatching MAXO NCIT
MAXO:0001269 clinical biopsy oio:hasDbXref OBI:0002650 biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001269 clinical biopsy oio:hasDbXref OBI:0002650 biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001270 clinical computed tomography assisted biopsy oio:hasDbXref OBI:0002652 computed tomography assisted biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001270 clinical computed tomography assisted biopsy oio:hasDbXref OBI:0002652 computed tomography assisted biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001271 clinical core needle biopsy oio:hasDbXref OBI:0002656 core needle biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001271 clinical core needle biopsy oio:hasDbXref OBI:0002656 core needle biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001272 clinical fine needle aspiration biopsy oio:hasDbXref OBI:0002655 fine needle aspiration biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001272 clinical fine needle aspiration biopsy oio:hasDbXref OBI:0002655 fine needle aspiration biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001273 clinical image guided biopsy oio:hasDbXref OBI:0002651 image guided biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001273 clinical image guided biopsy oio:hasDbXref OBI:0002651 image guided biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001274 clinical needle biopsy oio:hasDbXref OBI:0002654 needle biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001274 clinical needle biopsy oio:hasDbXref OBI:0002654 needle biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001275 clinical surgical biopsy oio:hasDbXref OBI:0002657 surgical biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001275 clinical surgical biopsy oio:hasDbXref OBI:0002657 surgical biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001276 clinical ultrasound-guided needle biopsy oio:hasDbXref OBI:0002653 ultrasound-guided needle biopsy semapv:UnspecifiedMatching MAXO OBI
MAXO:0001276 clinical ultrasound-guided needle biopsy oio:hasDbXref OBI:0002653 ultrasound-guided needle biopsy semapv:UnspecifiedMatching MAXO OBI
[40]:
maxo mappings l~biopsy -O sssom -o output/maxo-biopsy.sssom.tsv
[41]:
df = pd.read_csv("output/maxo-biopsy.sssom.tsv", sep="\t", comment="#").fillna("")
[42]:
df
[42]:
| subject_id | subject_label | predicate_id | object_id | object_label | mapping_justification | subject_source | object_source | |
|---|---|---|---|---|---|---|---|---|
| 0 | MAXO:0000332 | biopsy of anus | oio:hasDbXref | NCIT:C51586 | semapv:UnspecifiedMatching | MAXO | NCIT | |
| 1 | MAXO:0001269 | clinical biopsy | oio:hasDbXref | OBI:0002650 | biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 2 | MAXO:0001269 | clinical biopsy | oio:hasDbXref | OBI:0002650 | biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 3 | MAXO:0001270 | clinical computed tomography assisted biopsy | oio:hasDbXref | OBI:0002652 | computed tomography assisted biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 4 | MAXO:0001270 | clinical computed tomography assisted biopsy | oio:hasDbXref | OBI:0002652 | computed tomography assisted biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 5 | MAXO:0001271 | clinical core needle biopsy | oio:hasDbXref | OBI:0002656 | core needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 6 | MAXO:0001271 | clinical core needle biopsy | oio:hasDbXref | OBI:0002656 | core needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 7 | MAXO:0001272 | clinical fine needle aspiration biopsy | oio:hasDbXref | OBI:0002655 | fine needle aspiration biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 8 | MAXO:0001272 | clinical fine needle aspiration biopsy | oio:hasDbXref | OBI:0002655 | fine needle aspiration biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 9 | MAXO:0001273 | clinical image guided biopsy | oio:hasDbXref | OBI:0002651 | image guided biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 10 | MAXO:0001273 | clinical image guided biopsy | oio:hasDbXref | OBI:0002651 | image guided biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 11 | MAXO:0001274 | clinical needle biopsy | oio:hasDbXref | OBI:0002654 | needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 12 | MAXO:0001274 | clinical needle biopsy | oio:hasDbXref | OBI:0002654 | needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 13 | MAXO:0001275 | clinical surgical biopsy | oio:hasDbXref | OBI:0002657 | surgical biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 14 | MAXO:0001275 | clinical surgical biopsy | oio:hasDbXref | OBI:0002657 | surgical biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 15 | MAXO:0001276 | clinical ultrasound-guided needle biopsy | oio:hasDbXref | OBI:0002653 | ultrasound-guided needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
| 16 | MAXO:0001276 | clinical ultrasound-guided needle biopsy | oio:hasDbXref | OBI:0002653 | ultrasound-guided needle biopsy | semapv:UnspecifiedMatching | MAXO | OBI |
[44]:
maxo -a sqlite:obo:ncit lexmatch l~biopsy -o output/maxo-lexmatch-ncit-biopsy.sssom.tsv
WARNING:root:Skipping <urn:swrl#A> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#B> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#C> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#D> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#a1> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#a2> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#d> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#e> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#eff> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#g1> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#g2> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#in> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#mf2> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#mf> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#p> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#w> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#x> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#y> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl#z> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#p> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#q> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#u> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#x> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#y> as it is not a valid CURIE
WARNING:root:Skipping <urn:swrl:var#z> as it is not a valid CURIE
[45]:
df = pd.read_csv("output/maxo-lexmatch-ncit-biopsy.sssom.tsv", sep="\t", comment="#").fillna("")
df
[45]:
| subject_id | subject_label | predicate_id | object_id | object_label | mapping_justification | mapping_tool | confidence | subject_match_field | object_match_field | match_string | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | MAXO:0000332 | biopsy of anus | skos:closeMatch | NCIT:C51586 | Biopsy of Anus | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of anus |
| 1 | MAXO:0000332 | biopsy of anus | skos:closeMatch | NCIT:C51586 | Biopsy of Anus | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of anus |
| 2 | MAXO:0000336 | biopsy of bone marrow | skos:closeMatch | NCIT:C15193 | Bone Marrow Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of bone marrow |
| 3 | MAXO:0000336 | biopsy of bone marrow | skos:closeMatch | NCIT:C15193 | Bone Marrow Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | bone marrow biopsy |
| 4 | MAXO:0000336 | biopsy of bone marrow | skos:closeMatch | NCIT:C15193 | Bone Marrow Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | bone marrow biopsy |
| 5 | MAXO:0000336 | biopsy of bone marrow | skos:closeMatch | NCIT:C15193 | Bone Marrow Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | bone marrow biopsy |
| 6 | MAXO:0000338 | biopsy of brain | skos:closeMatch | NCIT:C51766 | Biopsy of Brain | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of brain |
| 7 | MAXO:0000338 | biopsy of brain | skos:closeMatch | NCIT:C51766 | Biopsy of Brain | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of brain |
| 8 | MAXO:0000338 | biopsy of brain | skos:closeMatch | NCIT:C51766 | Biopsy of Brain | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | brain biopsy |
| 9 | MAXO:0000340 | biopsy of breast | skos:closeMatch | NCIT:C51698 | Biopsy of Breast | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of breast |
| 10 | MAXO:0000340 | biopsy of breast | skos:closeMatch | NCIT:C51698 | Biopsy of Breast | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | breast biopsy |
| 11 | MAXO:0000340 | biopsy of breast | skos:closeMatch | NCIT:C51698 | Biopsy of Breast | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of breast |
| 12 | MAXO:0000341 | biopsy of bronchus | skos:closeMatch | NCIT:C51782 | Bronchial Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of bronchus |
| 13 | MAXO:0000350 | biopsy of colon | skos:closeMatch | NCIT:C51678 | Biopsy of Colon | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of colon |
| 14 | MAXO:0000350 | biopsy of colon | skos:closeMatch | NCIT:C51678 | Biopsy of Colon | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of colon |
| 15 | MAXO:0000355 | biopsy of duodenum | skos:closeMatch | NCIT:C51683 | Biopsy of Duodenum | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of duodenum |
| 16 | MAXO:0000355 | biopsy of duodenum | skos:closeMatch | NCIT:C51683 | Biopsy of Duodenum | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of duodenum |
| 17 | MAXO:0000359 | biopsy of esophagus | skos:closeMatch | NCIT:C51686 | Esophageal Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of esophagus |
| 18 | MAXO:0000366 | biopsy of heart | skos:closeMatch | NCIT:C51794 | Biopsy of Heart | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of heart |
| 19 | MAXO:0000366 | biopsy of heart | skos:closeMatch | NCIT:C51794 | Biopsy of Heart | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of heart |
| 20 | MAXO:0000373 | biopsy of larynx | skos:closeMatch | NCIT:C51663 | Biopsy of Larynx | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of larynx |
| 21 | MAXO:0000373 | biopsy of larynx | skos:closeMatch | NCIT:C51663 | Biopsy of Larynx | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of larynx |
| 22 | MAXO:0000375 | biopsy of lip | skos:closeMatch | NCIT:C51653 | Biopsy of Lip | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of lip |
| 23 | MAXO:0000375 | biopsy of lip | skos:closeMatch | NCIT:C51653 | Biopsy of Lip | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of lip |
| 24 | MAXO:0000376 | biopsy of liver | skos:closeMatch | NCIT:C51677 | Liver Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of liver |
| 25 | MAXO:0000376 | biopsy of liver | skos:closeMatch | NCIT:C51677 | Liver Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | liver biopsy |
| 26 | MAXO:0000376 | biopsy of liver | skos:closeMatch | NCIT:C51677 | Liver Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | liver biopsy |
| 27 | MAXO:0000380 | biopsy of lung | skos:closeMatch | NCIT:C51748 | Lung Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of lung |
| 28 | MAXO:0000380 | biopsy of lung | skos:closeMatch | NCIT:C51748 | Lung Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | lung biopsy |
| 29 | MAXO:0000380 | biopsy of lung | skos:closeMatch | NCIT:C51748 | Lung Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | lung biopsy |
| 30 | MAXO:0000380 | biopsy of lung | skos:closeMatch | NCIT:C51748 | Lung Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | lung biopsy |
| 31 | MAXO:0000381 | biopsy of lymph node | skos:closeMatch | NCIT:C51900 | Lymph Node Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of lymph node |
| 32 | MAXO:0000381 | biopsy of lymph node | skos:closeMatch | NCIT:C51900 | Lymph Node Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | lymph node biopsy |
| 33 | MAXO:0000381 | biopsy of lymph node | skos:closeMatch | NCIT:C51900 | Lymph Node Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | lymph node biopsy |
| 34 | MAXO:0000385 | biopsy of mouth | skos:closeMatch | NCIT:C51895 | Muscle Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | muscle biopsy |
| 35 | MAXO:0000385 | biopsy of mouth | skos:closeMatch | NCIT:C51895 | Muscle Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | muscle biopsy |
| 36 | MAXO:0000385 | biopsy of mouth | skos:closeMatch | NCIT:C51650 | Biopsy of Mouth | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of mouth |
| 37 | MAXO:0000385 | biopsy of mouth | skos:closeMatch | NCIT:C51650 | Biopsy of Mouth | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of mouth |
| 38 | MAXO:0000386 | biopsy of muscle | skos:closeMatch | NCIT:C51895 | Muscle Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of muscle |
| 39 | MAXO:0000389 | biopsy of nasopharynx | skos:closeMatch | NCIT:C51768 | Biopsy of Nasopharynx | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of nasopharynx |
| 40 | MAXO:0000389 | biopsy of nasopharynx | skos:closeMatch | NCIT:C51768 | Biopsy of Nasopharynx | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of nasopharynx |
| 41 | MAXO:0000392 | biopsy of pancreas | skos:closeMatch | NCIT:C51671 | Biopsy of Pancreas | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of pancreas |
| 42 | MAXO:0000392 | biopsy of pancreas | skos:closeMatch | NCIT:C51671 | Biopsy of Pancreas | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of pancreas |
| 43 | MAXO:0000395 | biopsy of peritoneum | skos:closeMatch | NCIT:C51627 | Biopsy of Peritoneum | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of peritoneum |
| 44 | MAXO:0000395 | biopsy of peritoneum | skos:closeMatch | NCIT:C51627 | Biopsy of Peritoneum | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of peritoneum |
| 45 | MAXO:0000397 | biopsy of pleura | skos:closeMatch | NCIT:C51897 | Pleural Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of pleura |
| 46 | MAXO:0000398 | biopsy of rectum | skos:closeMatch | NCIT:C51693 | Rectal Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of rectum |
| 47 | MAXO:0000403 | biopsy of small intestine | skos:closeMatch | NCIT:C51600 | Biopsy of Small Intestine | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of small intestine |
| 48 | MAXO:0000403 | biopsy of small intestine | skos:closeMatch | NCIT:C51600 | Biopsy of Small Intestine | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of small intestine |
| 49 | MAXO:0000406 | biopsy of stomach | skos:closeMatch | NCIT:C51685 | Gastric Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of stomach |
| 50 | MAXO:0000409 | biopsy of testis | skos:closeMatch | NCIT:C51894 | Biopsy of Testis | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of testis |
| 51 | MAXO:0000409 | biopsy of testis | skos:closeMatch | NCIT:C51894 | Biopsy of Testis | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of testis |
| 52 | MAXO:0000411 | biopsy of thyroid gland | skos:closeMatch | NCIT:C51613 | Biopsy of Thyroid Gland | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of thyroid gland |
| 53 | MAXO:0000411 | biopsy of thyroid gland | skos:closeMatch | NCIT:C51613 | Biopsy of Thyroid Gland | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of thyroid gland |
| 54 | MAXO:0000412 | biopsy of tongue | skos:closeMatch | NCIT:C51930 | Biopsy of Tongue | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of tongue |
| 55 | MAXO:0000412 | biopsy of tongue | skos:closeMatch | NCIT:C51930 | Biopsy of Tongue | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of tongue |
| 56 | MAXO:0000414 | biopsy of trachea | skos:closeMatch | NCIT:C51631 | Biopsy of Trachea | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of trachea |
| 57 | MAXO:0000414 | biopsy of trachea | skos:closeMatch | NCIT:C51631 | Biopsy of Trachea | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of trachea |
| 58 | MAXO:0000418 | biopsy of urethra | skos:closeMatch | NCIT:C51640 | Biopsy of Urethra | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of urethra |
| 59 | MAXO:0000418 | biopsy of urethra | skos:closeMatch | NCIT:C51640 | Biopsy of Urethra | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy of urethra |
| 60 | MAXO:0000423 | biopsy of skin | skos:closeMatch | NCIT:C51692 | Skin Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of skin |
| 61 | MAXO:0000423 | biopsy of skin | skos:closeMatch | NCIT:C51692 | Skin Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | skin biopsy |
| 62 | MAXO:0000423 | biopsy of skin | skos:closeMatch | NCIT:C51692 | Skin Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | skin biopsy |
| 63 | MAXO:0000755 | liquid biopsy | skos:closeMatch | NCIT:C135727 | Liquid Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | liquid biopsy |
| 64 | MAXO:0000755 | liquid biopsy | skos:closeMatch | NCIT:C135727 | Liquid Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | liquid biopsy |
| 65 | MAXO:0001121 | biopsy of kidney | skos:closeMatch | NCIT:C51699 | Kidney Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | biopsy of kidney |
| 66 | MAXO:0001121 | biopsy of kidney | skos:closeMatch | NCIT:C51699 | Kidney Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | kidney biopsy |
| 67 | MAXO:0001121 | biopsy of kidney | skos:closeMatch | NCIT:C51699 | Kidney Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | kidney biopsy |
| 68 | NCIT:C137909 | Computed Tomography Assisted Biopsy | skos:closeMatch | OBI:0002652 | computed tomography assisted biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | computed tomography assisted biopsy |
| 69 | NCIT:C137909 | Computed Tomography Assisted Biopsy | skos:closeMatch | OBI:0002652 | computed tomography assisted biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | computed tomography assisted biopsy |
| 70 | NCIT:C15189 | Biopsy | skos:closeMatch | OBI:0002650 | biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | biopsy |
| 71 | NCIT:C15189 | Biopsy | skos:closeMatch | OBI:0002650 | biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | biopsy |
| 72 | NCIT:C15189 | Biopsy | skos:closeMatch | OBI:0002650 | biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | biopsy |
| 73 | NCIT:C15189 | Biopsy | skos:closeMatch | OBI:0002650 | biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | biopsy |
| 74 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | NCIT:C15680 | Core Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | needle biopsy |
| 75 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | OBI:0002654 | needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | needle biopsy |
| 76 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | OBI:0002654 | needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | needle biopsy |
| 77 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | OBI:0002654 | needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | needle biopsy |
| 78 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | NCIT:C15680 | Core Biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | oio:hasExactSynonym | needle biopsy |
| 79 | NCIT:C15190 | Needle Biopsy | skos:closeMatch | NCIT:C15680 | Core Biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | needle biopsy |
| 80 | NCIT:C15385 | Excisional Biopsy | skos:closeMatch | OBI:0002657 | surgical biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | surgical biopsy |
| 81 | NCIT:C15652 | Image Guided Biopsy | skos:closeMatch | OBI:0002651 | image guided biopsy | semapv:LexicalMatching | oaklib | 0.5 | rdfs:label | rdfs:label | image guided biopsy |
| 82 | NCIT:C15652 | Image Guided Biopsy | skos:closeMatch | OBI:0002651 | image guided biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | image guided biopsy |
| 83 | NCIT:C15680 | Core Biopsy | skos:closeMatch | OBI:0002654 | needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | needle biopsy |
| 84 | NCIT:C15680 | Core Biopsy | skos:closeMatch | OBI:0002656 | core needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | core needle biopsy |
| 85 | NCIT:C15680 | Core Biopsy | skos:closeMatch | OBI:0002656 | core needle biopsy | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | rdfs:label | core needle biopsy |
| 86 | NCIT:C174241 | EWS Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C177402 | GCT Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
| 87 | NCIT:C174241 | EWS Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C179482 | OS Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
| 88 | NCIT:C174241 | EWS Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C186321 | HL Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
| 89 | NCIT:C177402 | GCT Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C179482 | OS Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
| 90 | NCIT:C177402 | GCT Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C186321 | HL Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
| 91 | NCIT:C179482 | OS Biopsy/Surgical Procedures Table | skos:closeMatch | NCIT:C186321 | HL Biopsy/Surgical Procedures Table | semapv:LexicalMatching | oaklib | 0.5 | oio:hasExactSynonym | oio:hasExactSynonym | biopsy/surgical procedures table |
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