# info.description
The deposits API allows to retrieve all deposits (documents and data) published by EFSA. The API users can access from a unique standard interface all the EFSA depositions stored in different repositories. The API returns the metadata either in Dublin Core standard (dc) or in EFSA specific format (Business Information Entity - bie).

# paths./.post.description
This API allows to retrieve metadata of EFSA published documents.
Metadata can be expressed in Dublin Core (dc) or EFSA Business Information Entity (bie).
In order to retrieve metadata it is possible to execute a query on the following list of fields:

BIE: title, type, abstract, content_doi, keywords, affiliation, publication_author, published_date, correspondence, language, publisher, publication_issn, journal_number, panel_members, question_number, adoption_date, acknowledgment, disclaimer_text, volume_number, issue_number

Dublin Core: title, type, description, identifier, subject, rightsHolder, creator, issued, language, contributor, rights, relation, publisher, isRequiredBy, format

To retrieve metadata expressed in Dublin Core insert metadata_format=dc.
To retrieve metadata expressed in EFSA Business Information Entity insert metadata_format=bie.
If metadata_format is omitted or contains a value different from the ones listed above, the response will not return metadata.

Below you can find some example of query search. For a complete guide on query syntax refers to https://docs.microsoft.com/en-us/rest/api/searchservice/search-documents



Search metadata of documents published after 31 january 2018:

Dublin Core
 { 
  "metadata_format": "dc",
  "top": "35",
  "skip": "0",
  "count": "true",
  "filter" : "issued gt 2018-01-31T00:00:00Z"
 }
 
Business Information Entity
 { 
  "metadata_format": "bie",
  "top": "35",
  "skip": "0",
  "count": "true",
  "filter" : "published_date gt 2018-01-31T00:00:00Z"
   }



Search metadata by document identifier:

Dublin Core
  { 
  "metadata_format": "dc",     
  "search": "identifier: \\"10.5281/zenodo.1255952 \\"", 
  "top": "10",
  "skip": "0",
  "count": "true",
  "queryType": "full"
   }

Business Information Entity
  { 
  "metadata_format": "bie",     
  "search": "content_doi:\\"10.5281/zenodo.1255952\\"", 
  "top": "10",
  "skip": "0",
  "count": "true",
  "queryType": "full"
   }   
   


Serach metadata of documents whose keywords and abstract contain the word bees or Apidae or honey:

Dublin Core 
 { 
  "metadata_format":"dc",
  "search": "subject:(bees || Apidae || honey) AND  description: (bees || Apidae || honey) ",
  "queryType": "full",
  "count":"true",
  "top":"10",
  "skip":"0"
  }
 
Business Information Entity
 { 
  "metadata_format":"bie",
  "search": "keywords:(bees || Apidae || honey) AND  abstract: (bees || Apidae || honey) ",
  "queryType": "full",
  "count":"true",
  "top":"10",
  "skip":"0"
  }

Please note: the GET method allows to execute the same actions of the above described POST method.

Furthermore please note that metadata currently returned by the API is retrieved form two different repositories: Zenodo and Wiley. By default when a search is executed it takes data from both sources. If you need to restrict the search to only one repository please use the "metadata_source" metadata. Accepted values for this metadata are 'zenodo' or 'wiley'.  Filtering by source requires as well to switch to the Lucene full query syntax via setting "queryType": "full". Below an example of query that restricts the search on Wiley repository

{ "metadata_format": "bie", "search": "keywords:welfare AND metadata_source:wiley", "count": "true", "top": "3", "skip": "0", "queryType": "full", "select":"keywords, content_doi" }

# paths./.post.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committee Of The Spanish Agency For Food Safety And Nutrition (Aesan) On The Role Of Nutrition In Autoimmune Diseases.

# paths./.post.responses.200.content.application/json.example.response.value[].description
The immune system is a network of cells, tissues, and organs that work together to defend the body
against attacks by “foreign” invaders. If pathogens survive the body’s front-line defenses, they still
have to find a way to escape a series of general defenses of the innate immune system, which are ready to attack without regard for specific antigen markers. These include patrolling phagocytes, natural killer T cells, and complement. Pathogens that cross the general barriers then confront specific weapons
of the adaptive immune system tailored just for them. (...) These tissues form the gut-associated lymphoid tissue and include the tonsils, adenoids, Peyer´s patches, lymphoid aggregates and appendix. (...) The result is called an
autoimmune disease. (...) The profound effect of diet on the immune system is well-known since many years ago. (...) In this regard, it has been established that: i) it is not yet possible to conclude whether caloric restriction improves the pathology of human autoimmune diseases; ii) polyunsaturated fatty acids seem to reduce autoimmune disease severity, however, its mechanisms of action is still unclear; iii) some dietary peptides and proteins are capable of inducing autoimmune diseases, such as celiac disease, type 1 diabetes and rheumatoid arthritis; iv) human studies investigating the effects of antioxidant vitamins, administered alone or together, have shown not quite significant benefits on clinical symptoms; v) vitamin D deficiency is associated with a higher risk of type 1 diabetes and multiple sclerosis. Deficiency
supplementation ameliorates this predisposition and vi) the few randomised, double-blind placebocontrolled
trials, with high doses of several probiotics strains, carried on patients with inflammatory bowel diseases, show a decrease in clinical inflammatory score, in medically treated patients. (...)

# paths./.post.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committee Of Aesan In Relation To The Microbiological Risks Associated With The Consumption Of Fruits Obtained From Fragaria And Rubus Spp.

# paths./.post.responses.200.content.application/json.example.response.value[].description
The consumption and as a result, the world production of fruits obtained from Fragaria spp. (such as
strawberries) or Rubus spp. (such as raspberries or blackberries) has significantly increased worldwide
in recent years. Spain is one of the largest producers of fruits from these plants, such as strawberries
and raspberries. It is therefore of great relevance to know the microbiological risks associated with the
consumption of these fruits, as well as the possible preventive measures to avoid the occurrence of
outbreaks derived from berries intake.
To the present, these fruits have caused outbreaks mainly due to the presence of viral agents
(especially norovirus and hepatitis A virus) and parasites (especially Cyclospora cayetanensis), whereas
in the case of bacterial pathogens it has only been documented one outbreak caused by Escherichia
coli O157: H7.
Given the heterogeneity of potentially contaminating pathogens in these products, and the fact that
they are usually eaten raw or minimally processed, it is difficult to establish disinfection protocols to
ensure their safety. For this reason, in order to maintain food security it is essential to maximize the
good hygienic practices in cultivation and harvesting, especially in fruits cultivated at ground level.
It is also necessary to maintain a standardized and internationally accepted traceability system that
allows a rapid identification of the causing agent when an outbreak caused by the consumption of
these fruits occurs.

# paths./.post.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committe Of Aesan About The Safety Criteria Applicable To The Content Of Domoic Acid In Scallops (Pecten Maximus) Harvesting

# paths./.post.responses.200.content.application/json.example.response.value[].description
Commission Decision 2002/226/EC of 15 March 2002 (UE, 2002) allows a restricted harvesting regime
of scallops with a domoic acid concentration in the whole body higher than 20 mg/kg. For this, two consecutive analyses of samples, taken between one and seven days maximum, must show that
the domoic acid concentration in the whole mollusk is lower than 250 mg/kg and that the DA concentration
in the parts intended for human consumption (muscle + gonad), which have to be analyzed separately, is lower than 4.6 mg/kg.
The Autonomous Community of Galicia proposes to include the analysis of muscle + gonad (the
edible part) as a basis for the checks of the harvesting in production areas, while maintaining the
same reference level of 4.6 mg/kg.
This Committee considers that the level of 4.6 mg/kg for the edible part (muscle + gonad) is safe
and can be used as a criterion in the checks of the harvesting of scallop.

# paths./.post.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./.post.responses.400.description
"response": {
  "error": {
    "code": "",
    "message": "Illegal arguments in query request: titles is not a searchable field."
  }
}

"response": {
  "error": {
    "code": "",
    "message": "Invalid expression: Could not find a property named 'published_dates' on type 'search.document'.\r\nParameter name: $filter"
  }
}

"response": {
  "error": {
    "code": "",
    "message": "Invalid expression: Syntax error at position 16 in 'published_date : 2018-01-31T00:00:00Z'.\r\nParameter name: $filter"
  }
}

"response":{ "error": { "code": "", "message": "The request is invalid. Invalid JSON." } }

# paths./*.get.description
This API allows to retrieve metadata of EFSA published documents.
Metadata can be expressed in Dublin Core (dc) or EFSA Business Information Entity (bie).
In order to retrieve metadata it is possible to execute a query on the following list of fields:

BIE: title, type, abstract, content_doi, keywords, affiliation, publication_author, published_date, correspondence, language, publisher, publication_issn, journal_number, panel_members, question_number, adoption_date, acknowledgment, disclaimer_text, volume_number, issue_number

Dublin Core: title, type, description, identifier, subject, rightsHolder, creator, issued, language, contributor, rights, relation, publisher, isRequiredBy, format

To retrieve metadata expressed in Dublin Core insert metadata_format=dc.
To retrieve metadata expressed in EFSA Business Information Entity insert metadata_format=bie.
If metadata_format contains a value different from the ones listed above, the response will not return metadata. If the metadata_format is not provided it will take by default the dc value.

Below you can find some example of query search. For a complete guide on query syntax refers to https://docs.microsoft.com/en-us/rest/api/searchservice/search-documents


Search metadata of documents published after 31 january 2018:

Dublin Core GET https://[endpoint]/?metadata_format=dc&$count=true&$top=10&$skip=0&$filter=issued gt 2018-01-31T00:00:00Z

Business Information Entity
GET https://[endpoint]/?metadata_format=bie&$count=true&$top=10&$skip=0&$filter=published_date gt 2018-01-19T00:00:00Z


Serach metadata of documents whose keywords and abstract contain the word bees or Apidae or honey:

Dublin Core
GET https://[endpoint]/?metadata_format=dc&$count=true&$top=10&$skip=0&search=subject:(bees || Apidae || honey) AND  description: (bees || Apidae || honey)&queryType=full

Business Information Entity
GET https://[endpoint]/?metadata_format=bie&$count=true&$top=10&$skip=0&search=keywords:(bees || Apidae || honey) AND  abstract: (bees || Apidae || honey)&queryType=full


Search metadata by document identifier:

Dublin Core 
GET https://[endpoint]/?metadata_format=dc&$count=true&$top=10&$skip=0&search=identifier:10.5281\\/zenodo.1255952&queryType=full&searchMode=all

Business Information Entity
GET https://[endpoint]/?metadata_format=bie&$count=true&$top=10&$skip=0&search=content_doi:10.5281\\/zenodo.1255952&queryType=full&searchMode=all


As an alternative way execute a search by identifier it is possible to call the endpoint url / identifier, for example if the identifier is "10.5281/zenodo.1255952" call

https://[endpoint]/10.5281/zenodo.1255952 

The response will be returned in Dublin Core standard.

If the endpoint is called without any request parameter, metadata belonging to the first 50 documents will be returned in Dublin Core standard.

Please note: the POST method allows to execute the same actions of the above described GET method.

Furthermore please note that metadata currently returned by the API is retrieved form two different repositories: Zenodo and Wiley. By default when a search is executed it takes data from both sources. If you need to restrict the search to only one repository please use the "metadata_source" metadata. Accepted values for this metadata are 'zenodo' or 'wiley'. Filtering by source requires as well to switch to the Lucene full query syntax via setting "queryType": "full". Below an example of query that restricts the search on Wiley repository

https://[endpoint]/?metadata_format=dc&$count=true&$top=3&$skip=0&search=subject:welfare AND metadata_source:wiley&queryType=full&$select=subject,identifier

# paths./*.get.parameters[].description
Dublin Core (dc) or Business Information Entities (bie)

# paths./*.get.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committee Of The Spanish Agency For Food Safety And Nutrition (Aesan) On The Role Of Nutrition In Autoimmune Diseases.

# paths./*.get.responses.200.content.application/json.example.response.value[].description
The immune system is a network of cells, tissues, and organs that work together to defend the body
against attacks by “foreign” invaders. If pathogens survive the body’s front-line defenses, they still
have to find a way to escape a series of general defenses of the innate immune system, which are ready to attack without regard for specific antigen markers. These include patrolling phagocytes, natural killer T cells, and complement. Pathogens that cross the general barriers then confront specific weapons
of the adaptive immune system tailored just for them. (...) These tissues form the gut-associated lymphoid tissue and include the tonsils, adenoids, Peyer´s patches, lymphoid aggregates and appendix. (...) The result is called an
autoimmune disease. (...) The profound effect of diet on the immune system is well-known since many years ago. (...) In this regard, it has been established that: i) it is not yet possible to conclude whether caloric restriction improves the pathology of human autoimmune diseases; ii) polyunsaturated fatty acids seem to reduce autoimmune disease severity, however, its mechanisms of action is still unclear; iii) some dietary peptides and proteins are capable of inducing autoimmune diseases, such as celiac disease, type 1 diabetes and rheumatoid arthritis; iv) human studies investigating the effects of antioxidant vitamins, administered alone or together, have shown not quite significant benefits on clinical symptoms; v) vitamin D deficiency is associated with a higher risk of type 1 diabetes and multiple sclerosis. Deficiency
supplementation ameliorates this predisposition and vi) the few randomised, double-blind placebocontrolled
trials, with high doses of several probiotics strains, carried on patients with inflammatory bowel diseases, show a decrease in clinical inflammatory score, in medically treated patients. (...)

# paths./*.get.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committee Of Aesan In Relation To The Microbiological Risks Associated With The Consumption Of Fruits Obtained From Fragaria And Rubus Spp.

# paths./*.get.responses.200.content.application/json.example.response.value[].description
The consumption and as a result, the world production of fruits obtained from Fragaria spp. (such as
strawberries) or Rubus spp. (such as raspberries or blackberries) has significantly increased worldwide
in recent years. Spain is one of the largest producers of fruits from these plants, such as strawberries
and raspberries. It is therefore of great relevance to know the microbiological risks associated with the
consumption of these fruits, as well as the possible preventive measures to avoid the occurrence of
outbreaks derived from berries intake.
To the present, these fruits have caused outbreaks mainly due to the presence of viral agents
(especially norovirus and hepatitis A virus) and parasites (especially Cyclospora cayetanensis), whereas
in the case of bacterial pathogens it has only been documented one outbreak caused by Escherichia
coli O157: H7.
Given the heterogeneity of potentially contaminating pathogens in these products, and the fact that
they are usually eaten raw or minimally processed, it is difficult to establish disinfection protocols to
ensure their safety. For this reason, in order to maintain food security it is essential to maximize the
good hygienic practices in cultivation and harvesting, especially in fruits cultivated at ground level.
It is also necessary to maintain a standardized and internationally accepted traceability system that
allows a rapid identification of the causing agent when an outbreak caused by the consumption of
these fruits occurs.

# paths./*.get.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.200.content.application/json.example.response.value[].title
Report Of The Scientific Committe Of Aesan About The Safety Criteria Applicable To The Content Of Domoic Acid In Scallops (Pecten Maximus) Harvesting

# paths./*.get.responses.200.content.application/json.example.response.value[].description
Commission Decision 2002/226/EC of 15 March 2002 (UE, 2002) allows a restricted harvesting regime
of scallops with a domoic acid concentration in the whole body higher than 20 mg/kg. For this, two consecutive analyses of samples, taken between one and seven days maximum, must show that
the domoic acid concentration in the whole mollusk is lower than 250 mg/kg and that the DA concentration
in the parts intended for human consumption (muscle + gonad), which have to be analyzed separately, is lower than 4.6 mg/kg.
The Autonomous Community of Galicia proposes to include the analysis of muscle + gonad (the
edible part) as a basis for the checks of the harvesting in production areas, while maintaining the
same reference level of 4.6 mg/kg.
This Committee considers that the level of 4.6 mg/kg for the edible part (muscle + gonad) is safe
and can be used as a criterion in the checks of the harvesting of scallop.

# paths./*.get.responses.200.content.application/json.example.response.value[].rightsholder[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.200.content.application/json.example.response.value[].creator[]
Spanish Agency for Consumer Affairs, Food Safety and Nutrition

# paths./*.get.responses.400.description
"response": { "error": { "code": "", "message": "Illegal arguments in query request: titles is not a searchable field." } }

"response": { "error": { "code": "", "message": "Invalid expression: Could not find a property named 'published_dates' on type 'search.document'.\r\nParameter name: $filter" } }

"response": { "error": { "code": "", "message": "Invalid expression: Syntax error at position 16 in 'published_date : 2018-01-31T00:00:00Z'.\r\nParameter name: $filter" } }