Documentation of LCRAnnotationsDB REST API

Our REST API allows to dowload data from our database programmatically. All request are send using POST method. To test it, please use available ReqBin or Advanced REST client tools.

Endpoints and their descriptions are in the table below.

Method

Endpoint

Description

POST

api/browse/

Post this endpoint in order to get general statistics about database, the same as in the page about databases .

Request this endpoint in order to get general informations about statistincs of database.

Item

Value

columns

Value is list of columns which are allowed to download. Available columns :

"dataset", "records_no", "source"

order

Value is dictionary with two keys: column and sign.

In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.

search_by_column

Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"columns": ["dataset", "records_no"],

"order": {"column":"Dataset", "sign":"desc"}

"search_by_column": {

"dataset": "Annotations"

}

POST

api/databases/

Get informations about annotations sources.

Request this endpoint in order to get general informations about sources.

Item

Value

columns

Value is list of columns which are allowed to download. Available columns :

'DatabaseID', 'Database name', 'Number of annotations'

order

Value is dictionary with two keys: column and sign.

In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.

search_by_column

Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"columns": ['DatabaseID', 'Database name', 'Number of annotations'],

"order": {"column":"Database name", "sign":"desc"}

"search_by_column": {

"Database name": "Disprot"

}

POST

api/proteins/

Get data about proteins, their LCRs or annotations.

Request this endpoint in order to get informations about LCRs, proteins or annotations in proteins.

Item	Value
result_data	This column depends from searched data. To get information about LCRs with searched annotation, value should be "lcrs", about annotations should be "annotations", about proteins should be "proteins".
columns	Value is list of columns which are allowed to download. For each result_data there are available columns for proteins: 'Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Protein Sequence', 'Protein header', 'Protein source', 'Number of LCRs', 'Number of annotations' Additionally, there are available columns depending from result_data value. It is possible to request for columns from analogous table: for result_data 'lcrs' there are available columns 'LCR ID', 'LCR Sequence', 'Start of LCR', 'End of LCR', 'LCR length', 'Identification method', 'Number of annotations' for result_data "annotations" there are available columns 'Annotation ID', 'Annotation', 'Category', 'Source ID', 'Gene Ontology', 'Start of annotation', 'End of annotation', 'Source database' for result_data "proteins" there are available columns only columns for table proteins
order	Value is dictionary with two keys: column and sign. In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.
search_by_column	Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"result_data": "lcrs",

"columns": ['Protein ID', 'LCR ID', 'LCR Sequence', 'Start of LCR, 'End of LCR', 'LCR length', 'Identification method'],

"order": {"column":"LCR ID", "sign":"desc"}

"search_by_column": {

'LCR ID': "500"

}

POST

api/lcrs/

Get informations about LCRs and their annotations.

Request this endpoint in order to get informations about LCRs or annotations of that LCRs.

Item	Value
result_data	This column depends from searched data. To get information about LCRs with searched annotation, value should be "lcrs", about annotations should be "annotations".
columns	For each result_data there are available columns for LCRs: 'LCR ID', 'LCR Sequence', 'Start of LCR, 'End of LCR', 'LCR length', 'Identification method', 'Number of annotations' Additionally, there are available columns depending from result_data value. It is possible to request for columns from analogous table: for result_data "annotations" there are available columns 'Annotation ID', 'Annotation', 'Category', 'Source ID', 'Gene Ontology', 'Start of annotation', 'End of annotation', 'Source database' for result_data "lcrs" there are available columns 'Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Protein Sequence', 'Protein header', 'Protein source', 'Number of LCRs', 'Number of annotations'
order	Value is dictionary with two keys: column and sign. In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.
search_by_column	Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"result_data": "lcrs",

"columns": ['LCR ID', 'Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Protein Sequence'],

"order": {"column":"UniProtACC", "sign":"desc"}

"search_by_column": {

"Protein name": "kinase"

}

POST

api/annotations/

Get informations about annotations or LCRs annotations.

Request this endpoint in order to get informations about annotations or annotations of lcrs.

Item	Value
result_data	This column depends from searched data. To get information about LCRs with searched annotation, value should be "lcrs", about annotations should be "annotations".
columns	Value is list of columns which are allowed to download. For each result_data there are available columns for annotations: 'Annotation ID', 'Annotation', 'Category', 'Source ID', 'Gene Ontology', 'Start of annotation', 'End of annotation', 'Source database', and for proteins: 'Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Protein Sequence', 'Protein header', 'Protein source', 'Number of LCRs', 'Number of annotations' Additionally, there are available columns depending from result_data value. It is possible to request for columns from analogous table: for result_data "lcrs" there are available columns 'LCR ID', 'LCR Sequence', 'Start of LCR', 'End of LCR', 'LCR length', 'Identification method', 'Number of annotations' for result_data "annotations" there are available columns 'Annotation ID', 'Annotation', 'Category', 'Source ID', 'Gene Ontology', 'Start of annotation', 'End of annotation', 'Source database'
order	Value is dictionary with two keys: column and sign. In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.
search_by_column	Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"result_data": "annotations",

"columns": [Annotation ID', 'Annotation', 'Category'],

"order": {"column":"Annotation", "sign":"desc"}

"search_by_column": {

"Annotation": "kinase"

}

POST

api/categories/

Get informations about categories of annotations from publications, databases and predictors.

Request this endpoint in order to get informations about categories of annotations or publications or protein annotations with a searched category.

Item	Value
result_data	This column depends from searched data. To get information about proteins, value should be "proteins", about annotations should be "annotations".
columns	Value is list of columns which are allowed to download. For each result_data there are available columns for categories: 'Category ID', 'Category', 'Gene ontology ID of category', 'Gene ontology name of category', 'Source of category', 'Number of LCRs by category', 'Number of annotations by category' Additionally, there are available columns depending from result_data value. It is possible to request for columns from analogous table: for result_data "proteins" there are available columns 'Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Protein Sequence', 'Protein header', 'Protein source', 'Number of LCRs', 'Number of annotations' for result_data "annotations" there are available columns 'Annotation ID', 'Annotation', 'Category', 'Source ID', 'Gene Ontology', 'Start of annotation', 'End of annotation', 'Source database' for result_data "categories" there are available columns for categories
order	Value is dictionary with two keys: column and sign. In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.
search_by_column	Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"result_data": "annotations",

"columns": ['Protein ID', 'UniProtACC', 'Organism', 'Protein name', 'Annotation ID', 'Annotation'],

"order": {"column":"Protein name", "sign":"desc"}

"search_by_column": {

"Annotation": "kinase"

}

Request this endpoint in order to get informations about publications and LCRs covered by them.

Item

Value

columns

Value is list of columns which are allowed to download. Available columns:

'UniProtACC', 'LCR start', 'LCR end', 'Annotation start', 'Annotation end', 'Annotation name', 'Annotation category', 'DOI', 'Title', 'Authors'

order

Value is dictionary with two keys: column and sign.

In order to indicate sign use words 'desc' or 'asc'. Value of column should be one of columns from pool columns.

search_by_column

Value is dictionary with keys as column name and key as searched key in this column. Searched column must be in list of columns.

Example request:

{

"columns": ['UniProtACC', 'LCR start', 'LCR end', 'Annotation start', 'Annotation end', 'Annotation name', 'Annotation category', 'DOI', 'Title', 'Authors' ],

"order": {"column":"UniProtACC", "sign":"desc"}

"search_by_column": {

"Annotation name": ["kinase"]

}