Up-to-date mapping of COVID-19 treatment and vaccine development (covid19-help.org data dump)

The free database mapping COVID-19 treatment and vaccine development based on the global scientific research is available at https://covid19-help.org/.   

Files provided here are curated partial data exports in the form of .csv files or full data export as .sql script generated with pg_dump from our PostgreSQL 12 database. You can also find .png file with our ER diagram of tables in .sql file in this repository.

Structure of CSV files

*On our site, compounds are named as substances  

compounds.csv

1. Id - Unique identifier in our database (unsigned integer)

2. Name - Name of the Substance/Compound (string)

3. Marketed name - The marketed name of the Substance/Compound (string)

4. Synonyms - Known synonyms (string)

5. Description - Description (HTML code)

6. Dietary sources - Dietary sources where the Substance/Compound can be found (string)

7. Dietary sources URL - Dietary sources URL (string)

8. Formula - Compound formula (HTML code)

9. Structure image URL - Url to our website with the structure image (string)

10. Status - Status of approval (string)

11. Therapeutic approach - Approach in which Substance/Compound works (string)

12. Drug status - Availability of Substance/Compound (string)

13. Additional data - Additional data in stringified JSON format with data as prescribing information and note (string)

14. General information - General information about Substance/Compound (HTML code)

references.csv

1. Id - Unique identifier in our database (unsigned integer)

2. Impact factor - Impact factor of the scientific article (string)

3. Source title - Title of the scientific article (string)

4. Source URL - URL link of the scientific article (string)

5. Tested on species - What testing model was used for the study (string)

6. Published at - Date of publication of the scientific article (Date in ISO 8601 format)

clinical-trials.csv

1. Id - Unique identifier in our database (unsigned integer)

2. Title - Title of the clinical trial study (string)

3. Acronym title - Acronym of title of the clinical trial study (string)

4. Source id - Unique identifier in the source database

5. Source id optional - Optional identifier in other databases (string) 

6. Interventions - Description of interventions (string)

7. Study type - Type of the conducted study (string)

8. Study results - Has results? (string)

9. Phase - Current phase of the clinical trial (string)

10. Url - URL to clinical trial study page on clinicaltrials.gov (string)

11. Status - Status in which study currently is (string)

12. Start date - Date at which study was started (Date in ISO 8601 format)

13. Completion date - Date at which study was completed (Date in ISO 8601 format)

14. Additional data - Additional data in the form of stringified JSON with data as locations of study, study design, enrollment, age, outcome measures (string)

compound-reference-relations.csv

1. Reference id - Id of a reference in our DB (unsigned integer)

2. Compound id -  Id of a substance in our DB (unsigned integer)

3. Note -  Id of a substance in our DB (unsigned integer)

4. Is supporting - Is evidence supporting or contradictory (Boolean, true if supporting)

compound-clinical-trial.csv

1. Clinical trial id -  Id of a clinical trial in our DB (unsigned integer)

2. Compound id  - Id of a Substance/Compound in our DB (unsigned integer)

tags.csv

1. Id - Unique identifier in our database (unsigned integer)

2. Name - Name of the tag (string)

tags-entities.csv

1. Tag id - Id of a tag in our DB (unsigned integer)

2. Reference id - Id of a reference in our DB (unsigned integer)
    

API Specification

Our project also has an Open API that gives you access to our data in a format suitable for processing, particularly in JSON format.

https://covid19-help.org/api-specification 

Services are split into five endpoints:

• Substances - /api/substances

• References - /api/references

• Substance-reference relations - /api/substance-reference-relations

• Clinical trials - /api/clinical-trials

• Clinical trials-substances relations - /api/clinical-trials-substances

Method of providing data

• All dates are text strings formatted in compliance with ISO 8601 as YYYY-MM-DD

• If the syntax request is incorrect (missing or incorrectly formatted parameters) an HTTP 400 Bad Request response will be returned. The body of the response may include an explanation.

• Data updated_at (used for querying changed-from) refers only to a particular entity and not its logical relations. Example: If a new substance reference relation is added, but the substance detail has not changed, this is reflected in the substance reference relation endpoint where a new entity with id and current dates in created_at and updated_at fields will be added, but in substances or references endpoint nothing has changed.

The recommended way of sequential download

• During the first download, it is possible to obtain all data by entering an old enough date in the parameter value changed-from, for example: changed-from=2020-01-01 It is important to write down the date on which the receiving the data was initiated let’s say 2020-10-20

• For repeated data downloads, it is sufficient to receive only the records in which something has changed. It can therefore be requested with the parameter changed-from=2020-10-20 (example from the previous bullet). Again, it is important to write down the date when the updates were downloaded (eg. 2020-10-20). This date will be used in the next update (refresh) of the data.

Services for entities

List of endpoint URLs:

• /api/substances

• /api/references

• /api/substance-reference-relations

• /api/clinical-trials

• /api/clinical-trials-substances

Format of the request

All endpoints have these parameters in common:

• changed-from - a parameter to return only the entities that have been modified on a given date or later.

• continue-after-id - a parameter to return only the entities that have a larger ID than specified in the parameter.

• limit - a parameter to return only the number of records specified (up to 1000). The preset number is 100.

Request example:

/api/references?changed-from=2020-01-01&continue-after-id=1&limit=100

Format of the response

The response format is the same for all endpoints.

• number_of_remaining_ids - the number of remaining entities that meet the specified criteria but are not displayed on the page. An integer of virtually unlimited size.

• entities - an array of entity details in JSON format.

Response example:

{

    "number_of_remaining_ids" : 100,

    "entities" : [

        {

            "id": 3,

            "url": "https://www.ncbi.nlm.nih.gov/pubmed/32147628",

            "title": "Discovering drugs to treat coronavirus disease 2019 (COVID-19).",

            "impact_factor": "Discovering drugs to treat coronavirus disease 2019 (COVID-19).",

            "tested_on_species": "in silico",

            "publication_date": "2020-22-02",

            "created_at": "2020-30-03",

            "updated_at": "2020-31-03",

            "deleted_at": null

        },

        {

            "id": 4,

            "url": "https://www.ncbi.nlm.nih.gov/pubmed/32157862",

            "title": "CT Manifestations of Novel Coronavirus Pneumonia: A Case Report",

            "impact_factor": "CT Manifestations of Novel Coronavirus Pneumonia: A Case Report",

            "tested_on_species": "Patient",

            "publication_date": "2020-06-03",

                "created_at": "2020-30-03",

            "updated_at": "2020-30-03",

            "deleted_at": null

        },

    ]

}

Endpoint details

Substances

URL: /api/substances

Substances endpoint returns data in the format specified in Response example as an array of entities in JSON format specified in the entity format section.

Entity format:

• id - Unique identifier in our database (unsigned integer)

• name - Name of the Substance (string)

• description - Description (HTML code)

• phase_of_research - Phase of research (string)

• how_it_helps - How it helps (string)

• drug_status - Drug status (string)

• general_information - General information (HTML code)

• synonyms - Synonyms (string)

• marketed_as - "Marketed as" (string)

• dietary_sources - Dietary sources name (string)

• dietary_sources_url - Dietary sources URL (string)

• prescribing_information - Prescribing information as an array of JSON objects with description and URL attributes as strings

• formula - Formula (HTML code)

• created_at - Date when the entity was added to our database (Date in ISO 8601 format)

• updated_at - Date when the entity was last updated in our database (Date in ISO 8601 format)

• deleted_at - Date when the entity was deleted in our database (Date in ISO 8601 format)

References

URL: /api/references

References endpoint returns data in the format specified in Response example as an array of entities in JSON format specified in the entity format section.

Entity format:

• id - Unique identifier in our database (unsigned integer)

• url - URL link of the scientific article (string)

• title - Title of the scientific article (string)

• impact_factor - Impact factor of the scientific article (string)

• tested_on_species - What testing model was used for the study (string)

• publication_date - Date of publication of the scientific article (Date in ISO 8601 format)

• created_at - Date when the entity was added to our database (Date in ISO 8601 format)

• updated_at - Date when the entity was last updated in our database (Date in ISO 8601 format)

• deleted_at - Date when the entity was deleted in our database (Date in ISO 8601 format)

Reference-substance relation

URL: /api/substance-reference-relations

Reference substance relation endpoint returns data in the format specified in Response example as an array of entities in JSON format specified in the entity format section.

Entity format:

• id - Unique identifier in our database (unsigned integer)

• reference_id - Id of a reference in our DB (unsigned integer)

• substance_id - Id of a substance in our DB (unsigned integer)

• note - Specific note for this relation (string)

• supporting - Is evidence supporting or contradictory (Boolean, true if supporting)

• created_at - Date when the entity was added to our database (Date in ISO 8601 format)

• updated_at - Date when the entity was last updated in our database (Date in ISO 8601 format)

• deleted_at - Date when the entity was deleted in our database (Date in ISO 8601 format)

Clinical trials

URL: /api/clinical-trials

Reference substance relation endpoint returns data in the format specified in Response example as an array of entities in JSON format specified in the entity format section.

Entity format:

• id - Unique identifier in our database (unsigned integer)

• title - Title of clinical trial study

• acronym_title - Id of a substance in our DB (unsigned integer)

• source_id - Id of reference in original database (string)

• source_id_optional - Optional Id in original database (multiple strings delimited by ",")

• interventions - Description of intervention in study

• study_type - Type of clinical trial

• study_results - Current results of clinical trial

• phase - Phase in which the study currently the clinical trial is

• url - Url to clinical trial page

• status - Status of progress in clinical trial

• start_date - Start date of clinical trial

• completion_date - Completion date of clinical trial

• created_at - Date when the entity was created in our database (Date in ISO 8601 format)

• updated_at - Date when the entity was last updated in our database (Date in ISO 8601 format)

• deleted_at - Date when the entity was deleted in our database (Date in ISO 8601 format)

Clinical trial-substances

URL: /api/clinical-trials-substances

Reference substance relation endpoint returns data in the format specified in Response example as an array of entities in JSON format specified in the entity format section.

This entity doesn't have Unique identifier (ID) and for that reason, filtration parameter "continue after ID" was replaced with "offset" filter

• offset - Number of entities to skip and from beginning to getting next chunk of data

Entity format:

• clinical_trial_id - Id of a clinical trial in our DB (unsigned integer)

• substance_id - Id of a substance in our DB (unsigned integer)

• created_at - Date when the entity was added to our database (Date in ISO 8601 format)

• updated_at - Date when the entity was last updated in our database (Date in ISO 8601 format)

• deleted_at - Date when the entity was deleted in our database (Date in ISO 8601 format)

 

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