VMH API
The Virtual Metbabolic Human Web API
# Install the command line client
$ pip install coreapi-cli
biomarkers
list
API endpoint to view biomarker information. Biomarkers connect diseases and metabolites. In addition, biomarkers contain information on the variation and ranges of concentration, along with references from where this information was extracted.
Usage:
-
Get biomarker information for a specific disease:
https://www.vmh.life/_api/biomarkers/?disease=3MGA
For more details on how to use biomarker filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
disease | Biomarker evidence for given disease (abbreviation). |
metabolite | Biomarker evidence for given metabolite (abbreviation). |
value | Value states the variation of biomarker (Increased/Decreased). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action biomarkers list -p page=... -p page_size=... -p disease=... -p metabolite=... -p value=... -p search=... -p sort=...
read
API endpoint to view biomarker information. Biomarkers connect diseases and metabolites. In addition, biomarkers contain information on the variation and ranges of concentration, along with references from where this information was extracted.
Usage:
-
Get biomarker information for a specific disease:
https://www.vmh.life/_api/biomarkers/?disease=3MGA
For more details on how to use biomarker filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this biomarker. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
disease | Biomarker evidence for given disease (abbreviation). |
metabolite | Biomarker evidence for given metabolite (abbreviation). |
value | Value states the variation of biomarker (Increased/Decreased). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action biomarkers read -p id=... -p disease=... -p metabolite=... -p value=... -p search=... -p sort=...
bodylocations
list
API endpoint to view body locations where microbes are found.
Usage:
-
See body locations for a specific microbe:
https://www.vmh.life/_api/bodylocations/?microbe=Helicobacter_pylori_26695
For more details on how to use body location information data filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
bodyLocation | Get body location by name. |
microbe | Get body locations where a microbe is present (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action bodylocations list -p page=... -p page_size=... -p bodyLocation=... -p microbe=... -p search=... -p sort=...
read
API endpoint to view body locations where microbes are found.
Usage:
-
See body locations for a specific microbe:
https://www.vmh.life/_api/bodylocations/?microbe=Helicobacter_pylori_26695
For more details on how to use body location information data filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this body location. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
bodyLocation | Get body location by name. |
microbe | Get body locations where a microbe is present (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action bodylocations read -p id=... -p bodyLocation=... -p microbe=... -p search=... -p sort=...
carbmicrobe
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbe required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action carbmicrobe read -p microbe=...
compartments
list
API endpoint to view available compartments. Metabolite lists are in id numbers for simplification.
Usage:
-
Get compartments for specific metabolite:
https://www.vmh.life/_api/compartments/?metabolite=23cump
For more details on how to use compartment filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Compartment name. |
metabolite | Get compartments where metabolite (abbreviation) is present |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action compartments list -p page=... -p page_size=... -p name=... -p metabolite=... -p search=... -p sort=...
read
API endpoint to view available compartments. Metabolite lists are in id numbers for simplification.
Usage:
-
Get compartments for specific metabolite:
https://www.vmh.life/_api/compartments/?metabolite=23cump
For more details on how to use compartment filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this compartment. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Compartment name. |
metabolite | Get compartments where metabolite (abbreviation) is present |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action compartments read -p id=... -p name=... -p metabolite=... -p search=... -p sort=...
compgenstatus
list
API endpoint to view the information on comparative genomic analysis performed for microbe reconstructions.
Usage:
-
See comparative genomic analysis information for a specific microbe:
https://www.vmh.life/_api/compgenstatus/?microbe=Abiotrophia_defectiva_ATCC_49176
For more details on how to use comparative genomic information data filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
status | Get comparative genomic information by status. |
pathway | Get comparitive genomics curation status by pathway. |
microbe | Get comparative genomic curation status of a microbe (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action compgenstatus list -p page=... -p status=... -p pathway=... -p microbe=... -p search=... -p sort=...
read
API endpoint to view the information on comparative genomic analysis performed for microbe reconstructions.
Usage:
-
See comparative genomic analysis information for a specific microbe:
https://www.vmh.life/_api/compgenstatus/?microbe=Abiotrophia_defectiva_ATCC_49176
For more details on how to use comparative genomic information data filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this comp gen status. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
status | Get comparative genomic information by status. |
pathway | Get comparitive genomics curation status by pathway. |
microbe | Get comparative genomic curation status of a microbe (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action compgenstatus read -p id=... -p status=... -p pathway=... -p microbe=... -p search=... -p sort=...
components
list
Deprecated: API endpoint that was used for food nutrient information - replaced by Nutrition Data, available here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Component (nutrient) name. |
minval | Minimum value for food component (nutrient value). |
maxval | Maximum value for food component (nutrient value). |
food | Food identifier. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action components list -p page=... -p page_size=... -p name=... -p minval=... -p maxval=... -p food=... -p search=... -p sort=...
read
Deprecated: API endpoint that was used for food nutrient information - replaced by Nutrition Data, available here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this component. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Component (nutrient) name. |
minval | Minimum value for food component (nutrient value). |
maxval | Maximum value for food component (nutrient value). |
food | Food identifier. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action components read -p id=... -p name=... -p minval=... -p maxval=... -p food=... -p search=... -p sort=...
dietflux
list
API endpoint that allows to view fluxes from diets.
Usage:
-
Get fluxes from a specific diet
https://www.vmh.life/_api/dietflux/?diet=Vegetarian
-
Download fluxes in CSV (tip: page_size to increase size of the page to 100 and format to change to CSV)
https://www.vmh.life/_api/dietflux/?diet=Vegetarian&page_size=100&format=pcsv
For more details on how to use dietflux filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
diet | Diet name. |
reaction | Get diet fluxes for a specific reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action dietflux list -p page=... -p page_size=... -p diet=... -p reaction=... -p search=... -p sort=...
read
API endpoint that allows to view fluxes from diets.
Usage:
-
Get fluxes from a specific diet
https://www.vmh.life/_api/dietflux/?diet=Vegetarian
-
Download fluxes in CSV (tip: page_size to increase size of the page to 100 and format to change to CSV)
https://www.vmh.life/_api/dietflux/?diet=Vegetarian&page_size=100&format=pcsv
For more details on how to use dietflux filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this diet flux. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
diet | Diet name. |
reaction | Get diet fluxes for a specific reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action dietflux read -p id=... -p diet=... -p reaction=... -p search=... -p sort=...
diets
list
API endpoint that allows to view available diets in the database.
Usage:
-
Get a specific diet:
https://www.vmh.life/_api/diets/?name=Vegetarian
For more details on how to use diets filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Diet name. |
name__icontains | Diet name contains expression (case un-sensitive). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action diets list -p page=... -p page_size=... -p name=... -p name__icontains=... -p search=... -p sort=...
read
API endpoint that allows to view available diets in the database.
Usage:
-
Get a specific diet:
https://www.vmh.life/_api/diets/?name=Vegetarian
For more details on how to use diets filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this diet. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Diet name. |
name__icontains | Diet name contains expression (case un-sensitive). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action diets read -p id=... -p name=... -p name__icontains=... -p search=... -p sort=...
diseases
list
API endpoint to view diseases available in the database.
Usage:
-
Get a specific gene:
https://www.vmh.life/_api/diseases/?abbreviation=BS1
-
Search a disease:
https://www.vmh.life/_api/genes/?search=Barter
For more details on how to use gene filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
abbreviation | Disease abbreviation. |
name | Disease name. |
name__icontains | Disease name contains expression. |
omim | Get disease with given OMIM. |
dtype | Get diseases by disease type. |
reaction | Get diseases associated with reaction (abbreviation). |
gene | Get diseases associated with gene (gene number). |
biomarker | Get diseases associaated with biomarker (metabolite abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action diseases list -p page=... -p page_size=... -p abbreviation=... -p name=... -p name__icontains=... -p omim=... -p dtype=... -p reaction=... -p gene=... -p biomarker=... -p search=... -p sort=...
read
API endpoint to view diseases available in the database.
Usage:
-
Get a specific gene:
https://www.vmh.life/_api/diseases/?abbreviation=BS1
-
Search a disease:
https://www.vmh.life/_api/genes/?search=Barter
For more details on how to use gene filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this Disease. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
abbreviation | Disease abbreviation. |
name | Disease name. |
name__icontains | Disease name contains expression. |
omim | Get disease with given OMIM. |
dtype | Get diseases by disease type. |
reaction | Get diseases associated with reaction (abbreviation). |
gene | Get diseases associated with gene (gene number). |
biomarker | Get diseases associaated with biomarker (metabolite abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action diseases read -p id=... -p abbreviation=... -p name=... -p name__icontains=... -p omim=... -p dtype=... -p reaction=... -p gene=... -p biomarker=... -p search=... -p sort=...
drug
drugderivatives > list
API endpoint that allows iem biomarkers to be viewed.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
createdDate | |
updatedDate | |
drug_compound | |
drug | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action drug drugderivatives > list -p page=... -p page_size=... -p createdDate=... -p updatedDate=... -p drug_compound=... -p drug=... -p search=... -p sort=...
drugderivatives > read
API endpoint that allows iem biomarkers to be viewed.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this drug compound derivatives. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
createdDate | |
updatedDate | |
drug_compound | |
drug | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action drug drugderivatives > read -p id=... -p createdDate=... -p updatedDate=... -p drug_compound=... -p drug=... -p search=... -p sort=...
drugs
list
API endpoint that allows drugs to be viewed.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
createdDate | |
updatedDate | |
drug_abbr | |
drug_name | |
drug_class | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action drugs list -p page=... -p page_size=... -p createdDate=... -p updatedDate=... -p drug_abbr=... -p drug_name=... -p drug_class=... -p search=... -p sort=...
read
API endpoint that allows drugs to be viewed.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
drug_id required | A unique integer value identifying this drug. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
createdDate | |
updatedDate | |
drug_abbr | |
drug_name | |
drug_class | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action drugs read -p drug_id=... -p createdDate=... -p updatedDate=... -p drug_abbr=... -p drug_name=... -p drug_class=... -p search=... -p sort=...
evidence
list
API endpoint to view biofluid evidence for metabolites. Biomarkers connect diseases and metabolites. This endpoint provides information on the biofluid, condition, value of concentration, and the origin of the data provided.
Usage:
-
Get evidence data for a specific metabolite:
https://www.vmh.life/_api/evidence/?metabolite=pcholn204_hs
For more details on how to use evidence filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
biofluid | Biofluid where evidence was extracted. |
metabolite | Get evidence from a specific metabolite (by abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action evidence list -p page=... -p page_size=... -p biofluid=... -p metabolite=... -p search=... -p sort=...
read
API endpoint to view biofluid evidence for metabolites. Biomarkers connect diseases and metabolites. This endpoint provides information on the biofluid, condition, value of concentration, and the origin of the data provided.
Usage:
-
Get evidence data for a specific metabolite:
https://www.vmh.life/_api/evidence/?metabolite=pcholn204_hs
For more details on how to use evidence filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this evidence. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
biofluid | Biofluid where evidence was extracted. |
metabolite | Get evidence from a specific metabolite (by abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action evidence read -p id=... -p biofluid=... -p metabolite=... -p search=... -p sort=...
fermcarbon
list
API endpoint to view available thermodynamic information on reactions.
Usage:
-
Get thermodynamic information on a specific reaction reaction:
https://www.vmh.life/_api/reacdeltags/?reaction=HEX1
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
sourcetype__icontains | Select sourcetype between the values "Fermentation" or "Carbon sources" (case un-sensitive). |
sourcetype | Select sourcetype between the values "Fermentation" or "Carbon sources". |
metabolite | Get fermentation and carbon sourcess associated with metabolite (abbreviation). |
model | Get fermentation and carbon sourcess associated with microbe (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action fermcarbon list -p page=... -p page_size=... -p sourcetype__icontains=... -p sourcetype=... -p metabolite=... -p model=... -p search=... -p sort=...
read
API endpoint to view available thermodynamic information on reactions.
Usage:
-
Get thermodynamic information on a specific reaction reaction:
https://www.vmh.life/_api/reacdeltags/?reaction=HEX1
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this fermentation carbon sources. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
sourcetype__icontains | Select sourcetype between the values "Fermentation" or "Carbon sources" (case un-sensitive). |
sourcetype | Select sourcetype between the values "Fermentation" or "Carbon sources". |
metabolite | Get fermentation and carbon sourcess associated with metabolite (abbreviation). |
model | Get fermentation and carbon sourcess associated with microbe (reconstruction name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action fermcarbon read -p id=... -p sourcetype__icontains=... -p sourcetype=... -p metabolite=... -p model=... -p search=... -p sort=...
fermicrobe
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbe required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action fermicrobe read -p microbe=...
foodgroups
list
API endpoint to view food groups.
Usage:
-
Basic usage:
https://www.vmh.life/_api/foodgroups
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action foodgroups list -p page=... -p page_size=... -p search=... -p sort=...
read
API endpoint to view food groups.
Usage:
-
Basic usage:
https://www.vmh.life/_api/foodgroups
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this food group. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action foodgroups read -p id=... -p search=... -p sort=...
foods
list
API endpoint to view foods available in the database.
Usage:
-
Get all foods of a specific type (tip: %20 is the hex code for space):
https://www.vmh.life/_api/foods/?product_type=Pasta%20Dish
For more details on how to use food filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
food_id | Filter food by id. |
component_food_pair | Food component filter. This argument is 3 values separated by `,`. 1 - nutrient identifier; 2 - `=` or `<=` or `<=`; 3 - value of that nutrient. |
component_food_interval | Food component interval of value. Query arguments separated by `,` where 1- is nutrient identifier; 2 - min of interval; 3 - max of interval. |
name | Filter food by food name |
product_type | Filter food by food type. |
food_group | Filter food by good groups. |
sources | Filter food by food sources. |
food_id__icontains | Food id contains given expression. |
name__icontains | Food name contains given expression. |
product_type__icontains | Filter food by food type. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action foods list -p page=... -p page_size=... -p food_id=... -p component_food_pair=... -p component_food_interval=... -p name=... -p product_type=... -p food_group=... -p sources=... -p food_id__icontains=... -p name__icontains=... -p product_type__icontains=... -p search=... -p sort=...
read
API endpoint to view foods available in the database.
Usage:
-
Get all foods of a specific type (tip: %20 is the hex code for space):
https://www.vmh.life/_api/foods/?product_type=Pasta%20Dish
For more details on how to use food filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this food. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
food_id | Filter food by id. |
component_food_pair | Food component filter. This argument is 3 values separated by `,`. 1 - nutrient identifier; 2 - `=` or `<=` or `<=`; 3 - value of that nutrient. |
component_food_interval | Food component interval of value. Query arguments separated by `,` where 1- is nutrient identifier; 2 - min of interval; 3 - max of interval. |
name | Filter food by food name |
product_type | Filter food by food type. |
food_group | Filter food by good groups. |
sources | Filter food by food sources. |
food_id__icontains | Food id contains given expression. |
name__icontains | Food name contains given expression. |
product_type__icontains | Filter food by food type. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action foods read -p id=... -p food_id=... -p component_food_pair=... -p component_food_interval=... -p name=... -p product_type=... -p food_group=... -p sources=... -p food_id__icontains=... -p name__icontains=... -p product_type__icontains=... -p search=... -p sort=...
genereactions
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
gene required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genereactions read -p gene=...
genes
list
API endpoint to view Human Genes available in the database.
Usage:
-
Get a specific gene:
https://www.vmh.life/_api/genes/?symbol=AOC3
https://www.vmh.life/_api/genes/?gene_number=8639.1
For more details on how to use gene filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
gene_number | Gene number. |
symbol | HGNC symbol. |
model | Reconstruction name. |
models | Set of reconstruction names separated by a comma. |
reaction | Reaction abbreviation. |
disease | Disease abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genes list -p page=... -p page_size=... -p gene_number=... -p symbol=... -p model=... -p models=... -p reaction=... -p disease=... -p search=... -p sort=...
read
API endpoint to view Human Genes available in the database.
Usage:
-
Get a specific gene:
https://www.vmh.life/_api/genes/?symbol=AOC3
https://www.vmh.life/_api/genes/?gene_number=8639.1
For more details on how to use gene filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
genes_id required | A unique integer value identifying this gene. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
gene_number | Gene number. |
symbol | HGNC symbol. |
model | Reconstruction name. |
models | Set of reconstruction names separated by a comma. |
reaction | Reaction abbreviation. |
disease | Disease abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genes read -p genes_id=... -p gene_number=... -p symbol=... -p model=... -p models=... -p reaction=... -p disease=... -p search=... -p sort=...
genesinmiccont
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbes required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genesinmiccont read -p microbes=...
genetomodel
list
API endpoint to view the connection between genes and reconstructions.
Usage:
-
Basic usage:
https://www.vmh.life/_api/genetomodel
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genetomodel list -p page=... -p page_size=... -p search=... -p sort=...
read
API endpoint to view the connection between genes and reconstructions.
Usage:
-
Basic usage:
https://www.vmh.life/_api/genetomodel
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this recon to gene. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action genetomodel read -p id=... -p search=... -p sort=...
langual
list
API endpoint to view the langual.
Usage:
-
Basic usage:
https://www.vmh.life/_api/langual
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action langual list -p page=... -p page_size=... -p search=... -p sort=...
read
API endpoint to view the langual.
Usage:
-
Basic usage:
https://www.vmh.life/_api/langual
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this langual. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action langual read -p id=... -p search=... -p sort=...
mealfood
list
API endpoint that allows to view food in diet meals.
Usage:
-
Get meal foods from a specific diet
https://www.vmh.life/_api/mealfood/?dietname=Vegetarian
For more details on how to use mealfood filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Name of the meal. |
dietname | Get meals from a given diet (name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action mealfood list -p page=... -p page_size=... -p name=... -p dietname=... -p search=... -p sort=...
read
API endpoint that allows to view food in diet meals.
Usage:
-
Get meal foods from a specific diet
https://www.vmh.life/_api/mealfood/?dietname=Vegetarian
For more details on how to use mealfood filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this meal food. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Name of the meal. |
dietname | Get meals from a given diet (name). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action mealfood read -p id=... -p name=... -p dietname=... -p search=... -p sort=...
meals
list
API endpoint that allows to view meal information from available diets.
Usage:
-
Get meals available in the database
https://www.vmh.life/_api/meals/
For more details on how to use meal filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action meals list -p page=... -p page_size=... -p search=... -p sort=...
read
API endpoint that allows to view meal information from available diets.
Usage:
-
Get meals available in the database
https://www.vmh.life/_api/meals/
For more details on how to use meal filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this meal. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action meals read -p id=... -p search=... -p sort=...
metabolites
list
API endpoint to view metabolites available in the database.
Usage:
-
Get a metabolite with a give abbreviation:
https://www.vmh.life/_api/metabolites/?abbreviation=h2o
-
Get that metabolite in json format:
https://www.vmh.life/_api/metabolites/?abbreviation=h2o&format=json
For more details on how to use metabolite filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
abbreviation__icontains | Metabolite abbreviation contains specified expression (case-unsensitive). |
abbreviation | Metabolite abbreviation |
hmdb | HMDB identifier. |
chargedFormula__icontains | Charged formula contains specified expression (case-unsensitive). |
chargedFormula | Neutral formula. |
fullName__icontains | Metabolite name contains specified expression (case-unsensitive). |
fullName | Metabolite name |
neutralFormula__icontains | Charged formula contains specified expression (case-unsensitive). |
neutralFormula | Neutral formula. |
isHuman | Set to 'True' if searching for metabolites in human metabolic reconstructions. |
inchiString__icontains | Inchi string contains specified expression (case-unsensitive). |
inchiString | Inchi string |
isMicrobe | Set to 'True' if searching for metabolites in human microbial reconstructions. |
model | Reconstruction name. |
organismtype | Reconstruction type: 'Microbe' or 'Human'. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metabolites list -p page=... -p page_size=... -p abbreviation__icontains=... -p abbreviation=... -p hmdb=... -p chargedFormula__icontains=... -p chargedFormula=... -p fullName__icontains=... -p fullName=... -p neutralFormula__icontains=... -p neutralFormula=... -p isHuman=... -p inchiString__icontains=... -p inchiString=... -p isMicrobe=... -p model=... -p organismtype=... -p search=... -p sort=...
read
API endpoint to view metabolites available in the database.
Usage:
-
Get a metabolite with a give abbreviation:
https://www.vmh.life/_api/metabolites/?abbreviation=h2o
-
Get that metabolite in json format:
https://www.vmh.life/_api/metabolites/?abbreviation=h2o&format=json
For more details on how to use metabolite filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
met_id required | A unique integer value identifying this metabolite. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
abbreviation__icontains | Metabolite abbreviation contains specified expression (case-unsensitive). |
abbreviation | Metabolite abbreviation |
hmdb | HMDB identifier. |
chargedFormula__icontains | Charged formula contains specified expression (case-unsensitive). |
chargedFormula | Neutral formula. |
fullName__icontains | Metabolite name contains specified expression (case-unsensitive). |
fullName | Metabolite name |
neutralFormula__icontains | Charged formula contains specified expression (case-unsensitive). |
neutralFormula | Neutral formula. |
isHuman | Set to 'True' if searching for metabolites in human metabolic reconstructions. |
inchiString__icontains | Inchi string contains specified expression (case-unsensitive). |
inchiString | Inchi string |
isMicrobe | Set to 'True' if searching for metabolites in human microbial reconstructions. |
model | Reconstruction name. |
organismtype | Reconstruction type: 'Microbe' or 'Human'. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metabolites read -p met_id=... -p abbreviation__icontains=... -p abbreviation=... -p hmdb=... -p chargedFormula__icontains=... -p chargedFormula=... -p fullName__icontains=... -p fullName=... -p neutralFormula__icontains=... -p neutralFormula=... -p isHuman=... -p inchiString__icontains=... -p inchiString=... -p isMicrobe=... -p model=... -p organismtype=... -p search=... -p sort=...
metcarbmicrobe
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbe required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metcarbmicrobe read -p microbe=...
metdeltags
list
API endpoint to view available thermodynamic information on metabolites.
Usage:
-
Get thermodynamic information on a specific metabolite:
https://www.vmh.life/_api/metdeltags/?metabolite=h2o
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
metabolite | Metabolite abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metdeltags list -p page=... -p page_size=... -p metabolite=... -p search=... -p sort=...
read
API endpoint to view available thermodynamic information on metabolites.
Usage:
-
Get thermodynamic information on a specific metabolite:
https://www.vmh.life/_api/metdeltags/?metabolite=h2o
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this met delta gs. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
metabolite | Metabolite abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metdeltags read -p id=... -p metabolite=... -p search=... -p sort=...
metfermicrobe
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbe required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metfermicrobe read -p microbe=...
metfromreac
read
API endpoint that allows to view all the Metabolites that takes part in a reaction.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metfromreac read -p abbr=...
metsinmiccont
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbes required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action metsinmiccont read -p microbes=...
microbecarfer
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
source required | |
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbecarfer read -p source=... -p abbr=...
microbegenereactions
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
gene required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbegenereactions read -p gene=...
microbegenes
list
API endpoint to view microbe genes.
Usage:
-
Get genes from a specific microbe:
https://www.vmh.life/_api/microbegenes/?model=Abiotrophia_defectiva_ATCC_49176
For more details on how to use microbe genes data filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
gene_number | Get microbe gene by gene number. |
model | Get genes in a given microbe (reconstruction name). |
reaction | Get microbe genes associated with a reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbegenes list -p page=... -p page_size=... -p gene_number=... -p model=... -p reaction=... -p search=... -p sort=...
read
API endpoint to view microbe genes.
Usage:
-
Get genes from a specific microbe:
https://www.vmh.life/_api/microbegenes/?model=Abiotrophia_defectiva_ATCC_49176
For more details on how to use microbe genes data filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this microbe gene. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
gene_number | Get microbe gene by gene number. |
model | Get genes in a given microbe (reconstruction name). |
reaction | Get microbe genes associated with a reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbegenes read -p id=... -p gene_number=... -p model=... -p reaction=... -p search=... -p sort=...
microbes
list
API endpoint to view available microbes in the database. This endpoint is associated with a reconstruction, but provides additional information on the organism, with emphasis on phylogenetic information, allowing users to customise queries to the microbiom resource.
Usage:
-
Get microbe from a reconstruction name:
https://www.vmh.life/_api/microbes/?reconstruction=Abiotrophia_defectiva_ATCC_49176
-
Get all microbes of a specific phylum:
https://www.vmh.life/_api/microbes/?phylum=Firmicutes
For more details on how to use microbe filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
organism | Filter microbe by organism. |
organism__icontains | Filter microbe by organism (case un-sensitive). |
seedid | Filter microbe by SEED ID. |
kingdom | Filter microbe by kingdom. |
phylum | Filter microbe by phylum. |
mclass | Filter microbe by class. |
order | Filter microbe by order. |
family | Filter microbe by family. |
reconstruction | Filter microbe by reconstruction name. |
reaction | Get microbes containing a reaction (reaction abbreviation). |
metabolite | Get microbes that contain the metabolite (use metabolite abbreviation). |
gene | Gene number to get microbe(s) with that gene. |
fermentationproduct | Filter microbes by abbreviation of metabolite that is a fermentation product. |
carbonsource | Filter microbes by the abbreviation of metabolite used as carbon source. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbes list -p page=... -p page_size=... -p organism=... -p organism__icontains=... -p seedid=... -p kingdom=... -p phylum=... -p mclass=... -p order=... -p family=... -p reconstruction=... -p reaction=... -p metabolite=... -p gene=... -p fermentationproduct=... -p carbonsource=... -p search=... -p sort=...
read
API endpoint to view available microbes in the database. This endpoint is associated with a reconstruction, but provides additional information on the organism, with emphasis on phylogenetic information, allowing users to customise queries to the microbiom resource.
Usage:
-
Get microbe from a reconstruction name:
https://www.vmh.life/_api/microbes/?reconstruction=Abiotrophia_defectiva_ATCC_49176
-
Get all microbes of a specific phylum:
https://www.vmh.life/_api/microbes/?phylum=Firmicutes
For more details on how to use microbe filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this microbe. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
organism | Filter microbe by organism. |
organism__icontains | Filter microbe by organism (case un-sensitive). |
seedid | Filter microbe by SEED ID. |
kingdom | Filter microbe by kingdom. |
phylum | Filter microbe by phylum. |
mclass | Filter microbe by class. |
order | Filter microbe by order. |
family | Filter microbe by family. |
reconstruction | Filter microbe by reconstruction name. |
reaction | Get microbes containing a reaction (reaction abbreviation). |
metabolite | Get microbes that contain the metabolite (use metabolite abbreviation). |
gene | Gene number to get microbe(s) with that gene. |
fermentationproduct | Filter microbes by abbreviation of metabolite that is a fermentation product. |
carbonsource | Filter microbes by the abbreviation of metabolite used as carbon source. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbes read -p id=... -p organism=... -p organism__icontains=... -p seedid=... -p kingdom=... -p phylum=... -p mclass=... -p order=... -p family=... -p reconstruction=... -p reaction=... -p metabolite=... -p gene=... -p fermentationproduct=... -p carbonsource=... -p search=... -p sort=...
microbesfrommetabolite
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbesfrommetabolite read -p abbr=...
microbesfromreaction
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action microbesfromreaction read -p abbr=...
mmass
list
API endpoint to view molecular mass of specific metabolites. This information is used to calculate the fluxes associated with designed diets. They have an associated component name (nutrient) and which metabolite and exchange reaction they are associated with.
Usage:
-
Get molecular mass for from a specific diet component
https://www.vmh.life/_api/mmass/?componentname=Alanine
-
The same result can also be obtained with reaction and metabolite abbreviations
https://www.vmh.life/_api/mmass/?reaction=EX_ala_L(e)
https://www.vmh.life/_api/mmass/?metabolite=ala_L
For more details on how to use molecular mass filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
componentname | |
reaction | |
metabolite | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action mmass list -p page=... -p page_size=... -p componentname=... -p reaction=... -p metabolite=... -p search=... -p sort=...
read
API endpoint to view molecular mass of specific metabolites. This information is used to calculate the fluxes associated with designed diets. They have an associated component name (nutrient) and which metabolite and exchange reaction they are associated with.
Usage:
-
Get molecular mass for from a specific diet component
https://www.vmh.life/_api/mmass/?componentname=Alanine
-
The same result can also be obtained with reaction and metabolite abbreviations
https://www.vmh.life/_api/mmass/?reaction=EX_ala_L(e)
https://www.vmh.life/_api/mmass/?metabolite=ala_L
For more details on how to use molecular mass filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this molecular mass. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
componentname | |
reaction | |
metabolite | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action mmass read -p id=... -p componentname=... -p reaction=... -p metabolite=... -p search=... -p sort=...
numchar
list
API endpoint to view numerical characteristics of microbe reconstruction.
Usage:
-
Get numerical characteristics for a specific reconstruction:
https://www.vmh.life/_api/numchar/?reconstruction=Abiotrophia_defectiva_ATCC_49176
For more details on how to use numerical characteristics filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
reconstruction | Reconstruction name. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action numchar list -p page=... -p page_size=... -p reconstruction=... -p search=... -p sort=...
read
API endpoint to view numerical characteristics of microbe reconstruction.
Usage:
-
Get numerical characteristics for a specific reconstruction:
https://www.vmh.life/_api/numchar/?reconstruction=Abiotrophia_defectiva_ATCC_49176
For more details on how to use numerical characteristics filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this num char. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
reconstruction | Reconstruction name. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action numchar read -p id=... -p reconstruction=... -p search=... -p sort=...
nutrients
list
API endpoint to view available nutrients in the database.
Usage:
-
Get a specific nutrient:
https://www.vmh.life/_api/nutrients/nut_no=USDA435
For more details on how to use nutrient filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
nut_no | Nutrient number. |
nut_no__icontains | Nutrient number contains expression. |
description | Nutrient description. |
common_name | Nutrient common name. |
category | Category of the nutrient. |
subcategory | Subcategory of the nutrient. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action nutrients list -p page=... -p page_size=... -p nut_no=... -p nut_no__icontains=... -p description=... -p common_name=... -p category=... -p subcategory=... -p search=... -p sort=...
read
API endpoint to view available nutrients in the database.
Usage:
-
Get a specific nutrient:
https://www.vmh.life/_api/nutrients/nut_no=USDA435
For more details on how to use nutrient filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this nutrient. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
nut_no | Nutrient number. |
nut_no__icontains | Nutrient number contains expression. |
description | Nutrient description. |
common_name | Nutrient common name. |
category | Category of the nutrient. |
subcategory | Subcategory of the nutrient. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action nutrients read -p id=... -p nut_no=... -p nut_no__icontains=... -p description=... -p common_name=... -p category=... -p subcategory=... -p search=... -p sort=...
nutritiondata
list
API endpoint to view food nutritional composition. It connects a specific food with a nutrient while providing the value of that nutrient per 100g.
Usage:
-
Get nutrition data for a specific food:
https://www.vmh.life/_api/nutritiondata/food=USDA10909
For more details on how to use nutrition data filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
food | |
nutrient | |
minval | |
maxval | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action nutritiondata list -p page=... -p page_size=... -p food=... -p nutrient=... -p minval=... -p maxval=... -p search=... -p sort=...
read
API endpoint to view food nutritional composition. It connects a specific food with a nutrient while providing the value of that nutrient per 100g.
Usage:
-
Get nutrition data for a specific food:
https://www.vmh.life/_api/nutritiondata/food=USDA10909
For more details on how to use nutrition data filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this nutrition data. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
food | |
nutrient | |
minval | |
maxval | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action nutritiondata read -p id=... -p food=... -p nutrient=... -p minval=... -p maxval=... -p search=... -p sort=...
organs
list
API endpoint to view available organs.
Usage:
-
Get a specific organ:
https://www.vmh.life/_api/numchar/?organ_abbreviation=heart
For more details on how to use Organ filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Get organ by name. |
organ_abbreviation | Get organ by its abbreviation. |
reaction | Get organs containing given reaction (abbreviation). |
metabolite | Get organs containing given metabolite (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action organs list -p page=... -p page_size=... -p name=... -p organ_abbreviation=... -p reaction=... -p metabolite=... -p search=... -p sort=...
read
API endpoint to view available organs.
Usage:
-
Get a specific organ:
https://www.vmh.life/_api/numchar/?organ_abbreviation=heart
For more details on how to use Organ filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this organ. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Get organ by name. |
organ_abbreviation | Get organ by its abbreviation. |
reaction | Get organs containing given reaction (abbreviation). |
metabolite | Get organs containing given metabolite (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action organs read -p id=... -p name=... -p organ_abbreviation=... -p reaction=... -p metabolite=... -p search=... -p sort=...
products
read
API endpoint that allows to view all the products of a given reaction.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action products read -p abbr=...
reacdeltags
list
API endpoint to view available thermodynamic information on reactions.
Usage:
-
Get thermodynamic information on a specific reaction reaction:
https://www.vmh.life/_api/reacdeltags/?reaction=HEX1
For more details on how to use filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
reaction | Reaction abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reacdeltags list -p page=... -p page_size=... -p reaction=... -p search=... -p sort=...
read
API endpoint to view available thermodynamic information on reactions.
Usage:
-
Get thermodynamic information on a specific reaction reaction:
https://www.vmh.life/_api/reacdeltags/?reaction=HEX1
For more details on how to use filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this reac delta gs. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
reaction | Reaction abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reacdeltags read -p id=... -p reaction=... -p search=... -p sort=...
reacfrommet
read
API endpoing that allows to view all the Reactions that a given metabolite (Abbreviation) takes part.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reacfrommet read -p abbr=...
reacfrommetmic
read
API endpoing that allows to view all the Reactions that a given metabolite (Abbreviation) takes part.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reacfrommetmic read -p abbr=...
reactants
read
API endpoint that allows to view all the reactants of a given reaction.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbr required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactants read -p abbr=...
reactionfromreactandproduct
read
API endpoint that allows to view all the reactions for a given reactants - a given product
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
abbrReactant required | |
abbrProduct required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactionfromreactandproduct read -p abbrReactant=... -p abbrProduct=...
reactiongenes
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
rid required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactiongenes read -p rid=...
reactionmicrobegenes
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
rid required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactionmicrobegenes read -p rid=...
reactions
list
API endpoint to view reactions available in the database.
Usage:
-
Get a reaction with a give abbreviation:
https://www.vmh.life/_api/reactions/?abbreviation=HEX1
-
Get that metabolite in json format:
https://www.vmh.life/_api/reacrions/?abbreviation=HEX1&format=json
For more details on how to use reaction filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
abbreviation__icontains | Reaction abbreviation contains specified expression (case-unsensitive). |
abbreviation | Reaction abbreviation. |
subsystem__icontains | Subsystem name contains specified expression (case-unsensitive). |
subsystem | Subsystem name. |
keggId | KEGG identifier. |
description__icontains | Reaction description contains specified expression (case-unsensitive). |
description | Reaction description. |
formula__icontains | Reaction formula contains specified expression (case-unsensitive). |
formula | Reaction formula. |
isHuman | Set to 'True' if searching for metabolites in human metabolic reconstructions. |
isMicrobe | Set to 'True' if searching for metabolites in human microbial reconstructions. |
ecnumber | E.C. number. |
model | Reconstruction name. |
disease | Disease abbreviation to get associated reactions. |
organismtype | Reconstruction type: 'Microbe' or 'Human'. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactions list -p page=... -p page_size=... -p abbreviation__icontains=... -p abbreviation=... -p subsystem__icontains=... -p subsystem=... -p keggId=... -p description__icontains=... -p description=... -p formula__icontains=... -p formula=... -p isHuman=... -p isMicrobe=... -p ecnumber=... -p model=... -p disease=... -p organismtype=... -p search=... -p sort=...
read
API endpoint to view reactions available in the database.
Usage:
-
Get a reaction with a give abbreviation:
https://www.vmh.life/_api/reactions/?abbreviation=HEX1
-
Get that metabolite in json format:
https://www.vmh.life/_api/reacrions/?abbreviation=HEX1&format=json
For more details on how to use reaction filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
rxn_id required | A unique integer value identifying this reaction. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
abbreviation__icontains | Reaction abbreviation contains specified expression (case-unsensitive). |
abbreviation | Reaction abbreviation. |
subsystem__icontains | Subsystem name contains specified expression (case-unsensitive). |
subsystem | Subsystem name. |
keggId | KEGG identifier. |
description__icontains | Reaction description contains specified expression (case-unsensitive). |
description | Reaction description. |
formula__icontains | Reaction formula contains specified expression (case-unsensitive). |
formula | Reaction formula. |
isHuman | Set to 'True' if searching for metabolites in human metabolic reconstructions. |
isMicrobe | Set to 'True' if searching for metabolites in human microbial reconstructions. |
ecnumber | E.C. number. |
model | Reconstruction name. |
disease | Disease abbreviation to get associated reactions. |
organismtype | Reconstruction type: 'Microbe' or 'Human'. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactions read -p rxn_id=... -p abbreviation__icontains=... -p abbreviation=... -p subsystem__icontains=... -p subsystem=... -p keggId=... -p description__icontains=... -p description=... -p formula__icontains=... -p formula=... -p isHuman=... -p isMicrobe=... -p ecnumber=... -p model=... -p disease=... -p organismtype=... -p search=... -p sort=...
reactiontomicrobegene
list
API endpoint to view connectiosn between reactions and microbe genes.
Usage:
-
Get connections for a specific reaction:
https://www.vmh.life/_api/reactiontomicrobegene/?reaction=1P4H2CBXLAH
For more details on how to use reaction to microbe gene connections data filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
reaction | Get reaction to microbe gene associations from reaction abbreviation. |
gene | Get reaction to microbe gene associations from microbe gene abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactiontomicrobegene list -p page=... -p page_size=... -p reaction=... -p gene=... -p search=... -p sort=...
read
API endpoint to view connectiosn between reactions and microbe genes.
Usage:
-
Get connections for a specific reaction:
https://www.vmh.life/_api/reactiontomicrobegene/?reaction=1P4H2CBXLAH
For more details on how to use reaction to microbe gene connections data filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this recon to microbe gene. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
reaction | Get reaction to microbe gene associations from reaction abbreviation. |
gene | Get reaction to microbe gene associations from microbe gene abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reactiontomicrobegene read -p id=... -p reaction=... -p gene=... -p search=... -p sort=...
reconstructions
list
API endpoint to view available reconstructions in the database.
Usage:
-
Get a specific reconstruction:
https://www.vmh.life/_api/reconstructions/?name=Recon
-
Get all microbe reconstructions
https://www.vmh.life/_api/reconstructions/?organismtype=Microbe
For more details on how to use reconstruction filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | Reconstruction name. |
descname | Descriptive name of the reconstruction. |
organism | Type of organism/reconstruction. |
organismtype | Type of organism: Human or Microbe. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reconstructions list -p page=... -p page_size=... -p name=... -p descname=... -p organism=... -p organismtype=... -p search=... -p sort=...
read
API endpoint to view available reconstructions in the database.
Usage:
-
Get a specific reconstruction:
https://www.vmh.life/_api/reconstructions/?name=Recon
-
Get all microbe reconstructions
https://www.vmh.life/_api/reconstructions/?organismtype=Microbe
For more details on how to use reconstruction filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
model_id required | A unique integer value identifying this reconstruction. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | Reconstruction name. |
descname | Descriptive name of the reconstruction. |
organism | Type of organism/reconstruction. |
organismtype | Type of organism: Human or Microbe. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action reconstructions read -p model_id=... -p name=... -p descname=... -p organism=... -p organismtype=... -p search=... -p sort=...
rxnsinmiccont
read
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
microbes required |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action rxnsinmiccont read -p microbes=...
rxntomodel
list
API endpoint to view connections between reactions and reconstructions. This connection provides information on reaction bounds in the reconstruction, GPR rule, confidence score, subsystem, references and notes.
Usage:
-
Get reaction information from Recon:
https://www.vmh.life/_api/rxntomodel/?model=Recon
-
Get all reconstruction connections of a specific reaction
https://www.vmh.life/_api/rxntomodel/?rxn=HEX1
For more details on how to use reconstruction filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
model | Reconstruction name. |
rxn | Reaction abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action rxntomodel list -p page=... -p page_size=... -p model=... -p rxn=... -p search=... -p sort=...
read
API endpoint to view connections between reactions and reconstructions. This connection provides information on reaction bounds in the reconstruction, GPR rule, confidence score, subsystem, references and notes.
Usage:
-
Get reaction information from Recon:
https://www.vmh.life/_api/rxntomodel/?model=Recon
-
Get all reconstruction connections of a specific reaction
https://www.vmh.life/_api/rxntomodel/?rxn=HEX1
For more details on how to use reconstruction filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this recon. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
model | Reconstruction name. |
rxn | Reaction abbreviation. |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action rxntomodel read -p id=... -p model=... -p rxn=... -p search=... -p sort=...
smatrix
list
API endpoint to view the connections between reactions and metabolites. This information represents the presence of a metabolite in a reaction. In addition it gives stoichiometry and compartment information of a metabolite in a reaction. Filters allow to get information on metabolites involved in reactions, and reactions that contain specific metabolites.
Usage:
-
Get all smatrix elements with a given metabolite abbreviation:
https://www.vmh.life/_api/smatrix/?metabolite=h2o
-
Get that smatrix elements of a specific reaction:
https://www.vmh.life/_api/smatrix/?reaction=HEX1
For more details on how to use smatrix filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
metabolite | Filter by metabolite (abrbeviation). |
reaction | Filter by reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action smatrix list -p page=... -p page_size=... -p metabolite=... -p reaction=... -p search=... -p sort=...
read
API endpoint to view the connections between reactions and metabolites. This information represents the presence of a metabolite in a reaction. In addition it gives stoichiometry and compartment information of a metabolite in a reaction. Filters allow to get information on metabolites involved in reactions, and reactions that contain specific metabolites.
Usage:
-
Get all smatrix elements with a given metabolite abbreviation:
https://www.vmh.life/_api/smatrix/?metabolite=h2o
-
Get that smatrix elements of a specific reaction:
https://www.vmh.life/_api/smatrix/?reaction=HEX1
For more details on how to use smatrix filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this smatrix. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
metabolite | Filter by metabolite (abrbeviation). |
reaction | Filter by reaction (abbreviation). |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action smatrix read -p id=... -p metabolite=... -p reaction=... -p search=... -p sort=...
subsystems
list
API endpoint to view reaction subsystem information.
Usage:
-
Get subsystem information for a specific subsystem (tip: %20 is the hex code for space):
https://www.vmh.life/_api/subsystems/?name=Alkaloid%20synthesis
For more details on how to use subsystem filters and live interaction with the API please see here.
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
page | A page number within the paginated result set. |
page_size | Number of results to return per page. |
name | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action subsystems list -p page=... -p page_size=... -p name=... -p search=... -p sort=...
read
API endpoint to view reaction subsystem information.
Usage:
-
Get subsystem information for a specific subsystem (tip: %20 is the hex code for space):
https://www.vmh.life/_api/subsystems/?name=Alkaloid%20synthesis
For more details on how to use subsystem filters and live interaction with the API please see here.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
id required | A unique integer value identifying this subsystem. |
Query Parameters
The following parameters should be included as part of a URL query string.
Parameter | Description |
---|---|
name | |
search | A search term. |
sort | Which field to use when ordering the results. |
# Load the schema document
$ coreapi get /_api/
# Interact with the API endpoint
$ coreapi action subsystems read -p id=... -p name=... -p search=... -p sort=...