Francis Kiptengwer Chemorion Marc-Antonio Bisotti https://creativecommons.org/licenses/by-sa/4.0/ This ontology provides a standardized approach for annotating URLs to support autonomous data curation agents in the biomedical domain. It includes detailed representations of URL components, parameters, and associated metadata. Towards Autonomous Data Curation Agents: A URL Annotation Standard 1.0 An Endpoint is a specific point of interaction within an API where resources are accessed or operations are performed. Describes the security or access limitations applied to the endpoint or API, such as authentication requirements. The root URL from which all endpoint paths are derived, serving as the base address for the API. Indicates the status code returned by the server to describe the outcome of the request. Common codes include 200 for success and 404 for not found. Provides a summary of what the API offers, detailing its main functionalities and use cases. Gives a link to a webpage with more detailed information about the endpoint. Classifies the type of Endpoint, such as RESTful or SOAP, based on its operational mechanics and structure. Defines a list of operational points under an API, where each Endpoint represents a specific functionality or data access point. Sample data demonstrating what the request body should look like, aiding in testing and implementation. HTTP methods are a set of request methods to indicate the desired action to be performed for a given resource. Each method implies a specific operation and HTTP semantics. A 32-bit number that identifies a specific interface on a network, using a dotted decimal format. A 128-bit address that allows a greater number of devices to be connected directly to the internet, noted for its colon-separated hexadecimal format. Domain names that include characters beyond the basic ASCII set, accommodating the full range of scripts and symbols used globally. The format of the media type expected by the request, commonly defined as MIME types. Denotes the formal name of the API, used for identification and reference. Parameters required for establishing authenticated communication between client and server, often as part of the header or URL query. Part of the credentials required for accessing a protected resource or service, not recommended to be used openly in URLs due to security concerns. Method for encoding information in a Uniform Resource Identifier (URI) under certain circumstances. Although commonly called URL encoding, it is, in fact, used more generally within the main Uniform Resource Identifier (URI) set, which includes both Uniform Resource Locator (URL) and Uniform Resource Name (URN). The port number associated with the server, directing traffic to specific services running on a host. Specifies the number of requests that can be made to an Endpoint within a given time frame, important for managing system load and service availability. A brief, standardized description of the status code, providing immediate insight into the result of the HTTP request. Characters that are reserved within a URL for special use within the scheme component, they must be encoded if they are to be used within the user data. Indicates the type of data or resource that the Endpoint handles, such as 'genomic data' or 'clinical trial information'. A definition or schema specifying the structure of the request body. It often follows a specified format such as JSON Schema or XML Schema. The method used for authenticating a request, such as Basic, Digest, or OAuth. Part of the domain that is a subset of a larger domain under the DNS hierarchy. Subdomains can represent different services or sections of a website. The highest level of the domain structure, such as '.com' or '.org', representing either the type of entity or geographical location. Components of the Uniform Resource Identifier (URI), where URL specifies location, URN specifies name, and IRI is an internationalized form of URI allowing characters from the universal character set. Characters that can be freely used in a URI without the need to be encoded. These characters are alphanumeric, and the special characters "-", ".", "_", and "~". The user identification used in conjunction with a password to gain access to a secured system or resource. Indicates the version of the API, helping to manage updates and compatibility. API_Name API_BaseURL API_Description Endpoint_Description API_Version Endpoint_AccessRestrictions Request_Auth_Parameters Request_Auth_Scheme URLComp_Authority_Host_DomainName_IDN URLComp_Authority_Host_DomainName_Subdomains URLComp_Authority_Host_DomainName_TLD URLComp_Authority_Host_IPAddress_IPv4 URLComp_Authority_Host_IPAddress_IPv6 URLComp_Authority_Port URLComp_Authority_UserInfo_Password URLComp_Authority_UserInfo_Username Request_Body_Examples Response_Body_Examples Request_Body_MediaType Response_Body_MediaType Request_Body_Schema Response_Body_Schema Request_ContentType Response_ContentType Endpoint_DocumentationURL URLComp_Fragment Request_Headers_Description Response_Headers_Description Request_Headers_Name Response_Headers_Name Request_Headers_Value Response_Headers_Value URI_IRI HTTPMethod Endpoint_Name URLComp_Path_Segments_DotSegments URLComp_Path_Segments_Static URLComp_Path_Segments_Variable Encoding_PercentEncoding URLComp_Query_Parameter_Description URLComp_Query_Parameter_Name URLComp_Query_Parameter_Required URLComp_Query_Parameter_Type URLComp_Query_Parameter_Value Endpoint_RateLimits Encoding_ReservedCharacters Endpoint_ResourceType URLComp_Scheme Response_StatusCode_Code Response_StatusCode_Description Response_StatusCode_ReasonPhrase Endpoint_Type URI_URL URI_URN Encoding_UnreservedCharacters ID ID ID ID ID ID ID ESearch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ Provides a list of UIDs matching a text query Searches and retrieves primary IDs and term translations 2 Public eutils.ncbi.nlm.nih.gov application/xml application/x-www-form-urlencoded https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch Content-Type application/xml GET ESearch esearch.fcgi %20 Database to search, search term db, term true string 3/sec, 10/sec with API key &,= PrimaryIDs https 200 Successful response OK Search https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi a-z, A-Z, 0-9 1 1 1 1 1 1 1 1.0 Francis Kiptengwer Chemorion Marc-Antonio Bisotti https://creativecommons.org/licenses/by-sa/4.0/ This ontology provides a standardized approach for annotating URLs to support autonomous data curation agents in the biomedical domain. It includes detailed representations of URL components, parameters, and associated metadata. Towards Autonomous Data Curation Agents: A URL Annotation Standard 1.0