19:06:2014 23:03 WSIO WSIO 1.2 032 Matus Kalas Acknowledgement for technical support: Torbjorn Lium, Lorand Janos Szentennai, Stanislav Oltu. Author: Matus Kalas, (c) 2011-2014, Computational Biology Unit, Department of Informatics, University of Bergen, Norway. Licence: Available under the Creative Commons BY-ND 3.0 licence with allowed attributed reference to, and import of, unmodified( PIs: Inge Jonassen, Kjell Petersen, Ibid. Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general. 'Created in' specificies the released version of the ontology since which the concept has been added and its ID created. http://edamontology.org/created_in WSIO created_in true created_in Created in 'Created in' specificies the released version of the ontology since which the concept has been added and its ID created. http://wsio.org 'Documentation' concept attribute ('documentation' metadata tag) is pointing to a page with explanation, description, documentation, or specification of the given data compression or encoding. http://edamontology.org/documentation Specification WSIO documentation true documentation Does not handle different versions of the specification or of the concept itself. Within WSIO, 'Documentation' applies to concrete forms of data transfer ('Transfer') and data compression/encoding ('Compression'). Documentation 'Documentation' concept attribute ('documentation' metadata tag) is pointing to a page with explanation, description, documentation, or specification of the given data compression or encoding. http://wsio.org Specification http://wsio.org 'Example' concept attribute ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. http://edamontology.org/example WSIO example true example Example 'Example' concept attribute ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. http://wsio.org 'Obsolete_since' specificies the released version of the ontology since which the concept has been obsolete. http://edamontology.org/obsolete_since WSIO obsolete_since true obsolete_since Obsolete Since 'Obsolete_since' specificies the released version of the ontology since which the concept has been obsolete. http://wsio.org 'Regular expression' concept attribute specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. http://edamontology.org/regex WSIO regex true regex Regular expression 'Regular expression' concept attribute specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. http://wsio.org definition antisymmetric property WSIO Compression sub-ontology The top-level-rooted WSIO 'Compression' sub-ontology includes forms of compression and binary-to-text encoding, and their combinations, that are relevant with respect to input and output data of Web services. Concepts of WSIO 'Compression' sub-ontology are applicable also outside of the context of Web-service interaction. WSIO concept properties Additional tags of metadata of WSIO concepts, or their trailing modifiers or qualifiers. Applicable also outside of the context of Web-service interaction. 'Concept URI' metadata tag in the OBO format ('! concept_uri: ') defines the canonical global URI of a concept. Global unique identifier Global Unified Resource Identifier (URI) WSIO concept_uri true Concept URI Global unique identifier http://wsio.org Global Unified Resource Identifier (URI) http://wsio.org 'Concept URI' metadata tag in the OBO format ('! concept_uri: ') defines the canonical global URI of a concept. http://wsio.org WSIO Data sub-ontology The top-level-rooted WSIO 'Data' sub-ontology includes types of data that are relevant with respect to interaction scenarios with Web services, including session handling (for example 'explicit polling' within asynchronous invocation). Concepts of WSIO 'Data' sub-ontology are applicable also outside of the context of Web-service interaction. 'Note' trailing modifier ('note=') of any concept or ontology attributes. Contains a note for a human reader related to the given attribute. WSIO note true Note 'Note' trailing modifier ('note=') of any concept or ontology attributes. Contains a note for a human reader related to the given attribute. http://wsio.org WSIO Operation sub-ontology The top-level-rooted WSIO 'Operation' sub-ontology includes operations that are relevant with respect to interaction scenarios with Web services, including session handling (for example 'explicit polling' within asynchronous invocation). Some concepts of WSIO 'Operation' sub-ontology are applicable also outside of the context of Web-service interaction. WSIO relation types Types of relations defined between concepts of WSIO, or available to be used for annotations of external entities' relations to concepts or external entities. All relation types are applicable also outside of the context of Web-service interaction. Supported by eSysbio Functionality denoted by these concepts is supported by the eSysbio system (http://esysbio.org) within the automated Web-service invocation and input/output data handling. WSIO Transfer sub-ontology The top-level-rooted WSIO 'Transfer' sub-ontology includes forms of transfer and transfer protocols that are relevant with respect to transferring input and output data to and from Web services. Some concepts of WSIO 'Transfer' sub-ontology are applicable also outside of the context of Web-service interaction. subset_property has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand 'A has_function B' defines for the subject A, that it has the object B as its function. false http://edamontology.org/has_function has_function WSIO bearer_of has_function true false false false false has_function Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of WSIO, 'has_function' serves only for relating annotated entities outside of WSIO with 'Operation' concepts. has function 'A has_function B' defines for the subject A, that it has the object B as its function. http://wsio.org has_function http://purl.obolibrary.org/obo/OBI_0000306 'OBI:has_function' only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes, with objects that are a 'function' (snap:Function). It does not define explicitly that the object is a function of the subject. bearer_of OBO_REL:bearer_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. false http://edamontology.org/has_input has_specified_input WSIO has_participant has_input true false false false false has_input Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In WSIO, only 'has_input' is explicitly defined between WSIO concepts, not the inverse 'is_input_of'. has input 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. http://wsio.org has_specified_input http://purl.obolibrary.org/obo/OBI_0000293 'OBI:has_specified_input' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). has_participant OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. false http://edamontology.org/has_output has_specified_output WSIO has_participant has_output true false false false false has_output Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In WSIO, only 'has_output' is explicitly defined between WSIO concepts, not the inverse 'is_output_of'. has output 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. http://wsio.org has_specified_output http://purl.obolibrary.org/obo/OBI_0000299 'OBI:has_specified_output' only relates subjects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011) with objects that are a 'continuant' (snap:Continuant). has_participant OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. 'A is_function_of B' defines for the subject A, that it is a function of the object B. false http://edamontology.org/is_function_of function_of WSIO inheres_in is_function_of true false false false false is_function_of Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within WSIO itself, 'is_function_of' is not used. is function of 'A is_function_of B' defines for the subject A, that it is a function of the object B. http://wsio.org function_of OBO_REL:function_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. inheres_in OBO_REL:inheres_in Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. false http://edamontology.org/is_input_of is_specified_input_of WSIO participates_in is_input_of true false false false false is_input_of Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In WSIO, 'is_input_of' is not explicitly defined between WSIO concepts, only the inverse 'has_input'. is input of 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. http://wsio.org is_specified_input_of http://purl.obolibrary.org/obo/OBI_0000295 'OBI:is_specified_input_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). participates_in OBO_REL:participates_in 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. false http://edamontology.org/is_output_of is_specified_output_of WSIO participates_in is_output_of true false false false false is_output_of Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In WSIO, 'is_output_of' is not explicitly defined between WSIO concepts, only the inverse 'has_output'. is output of 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. http://wsio.org is_specified_output_of http://purl.obolibrary.org/obo/OBI_0000312 'OBI:is_specified_output_of' only relates subjects that are a 'continuant' (snap:Continuant) with objects that are a 'planned process' (http://purl.obolibrary.org/obo/OBI_0000011). participates_in OBO_REL:participates_in 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. 'A has_compression B' defines for the subject A, that it has the object B as its compression (form of compression, compressed format), and/or binary-to-text encoding. false has transfer compression WSIO has_quality has_compression false false false false false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) an input, output, input argument, or output argument of an 'Operation'. Object B can either be a concept that is a 'Compression' (or has a 'Compression' function), or an entity outside of an ontology that has a 'Compression' function or is a 'Compression' (a compression/encoding method or format specification). In the scope of WSIO, 'has_compression' serves only for relating annotated entities outside of WSIO with 'Compression' concepts. has compression 'A has_compression B' defines for the subject A, that it has the object B as its compression (form of compression, compressed format), and/or binary-to-text encoding. http://wsio.org has transfer compression http://wsio.org has_quality http://purl.obolibrary.org/obo/OBI_0000298 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. 'A has_transfer B' defines for the subject A, that it has the object B as its transfer (form of transfer, transfer protocol). false WSIO has_quality has_transfer false false false false false Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) an input, output, input argument, or output argument of an 'Operation'. Object B can either be a concept that is a 'Transfer' (or has a 'Transfer' function), or an entity outside of an ontology that has a 'Transfer' function or is a 'Transfer' (a transfer specification). In the scope of WSIO, 'has_transfer' serves only for relating annotated entities outside of WSIO with 'Transfer' concepts. has transfer 'A has_transfer B' defines for the subject A, that it has the object B as its transfer (form of transfer, transfer protocol). http://wsio.org has_quality http://purl.obolibrary.org/obo/OBI_0000298 'OBI:has_quality' might be seen narrower in the sense that it only relates subjects that are an 'independent_continuant' (snap:IndependentContinuant) with objects that are a 'quality' (snap:Quality), and is broader in the sense that it relates with any qualities of the subject. 'A is_compression_of B' defines for the subject A, that it is a compression (form of compression, compressed format), and/or binary-to-text encoding, of the object B. false is transfer compression of WSIO quality_of is_compression_of false false false false false Subject A can either be a concept that is a 'Compression' (or has a 'Compression' function), or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has a 'Compression' function or is a 'Compression' (a compression/encoding method or format specification). Object B can be any concept or entity outside of an ontology that is (or is in a role of) an input, output, input argument, or output argument of an 'Operation'. Within WSIO itself, 'is_compression_of' is not used. is compression of 'A is_compression_of B' defines for the subject A, that it is a compression (form of compression, compressed format), and/or binary-to-text encoding, of the object B. http://wsio.org is transfer compression of http://wsio.org quality_of OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. 'A is_transfer_of B' defines for the subject A, that it is a transfer (form of transfer, transfer protocol) of the object B. false WSIO quality_of is_transfer_of false false false false false Subject A can either be a concept that is a 'Transfer' (or has a 'Transfer' function), or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has a 'Transfer' function or is a 'Transfer' (a transfer specification). Object B can be any concept or entity outside of an ontology that is (or is in a role of) an input, output, input argument, or output argument of an 'Operation'. Within WSIO itself, 'is_transfer_of' is not used. is transfer of 'A is_transfer_of B' defines for the subject A, that it is a transfer (form of transfer, transfer protocol) of the object B. http://wsio.org quality_of OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. Compression (form of data compression), a form of encoding of binary data, or a sequence of compression and encoding methods, are the ways data is compressed and/or eventually encoded to decrease its volume (and eventually be exchanged in text format). They imply the way compressed/encoded data should be decompressed/decoded to be readable in its original form again. continuant Data compression and encoding Data compression and/or encoding method Form of data compression and/or encoding Type of data compression and/or encoding Compressed and/or encoded data format WSIO Format Operation Process function process quality WSIO_compression:004 A top-level concept in WSIO rooting the 'Compression' sub-ontology. WSIO 'Compression' sub-ontology includes forms of compression and binary-to-text encoding, and their combinations, that are relevant with respect to input and output data of Web services. Concepts of WSIO 'Compression' sub-ontology are applicable also outside of the context of Web-service interaction. Compression or encoding WSIO:compression:004 Compression (form of data compression), a form of encoding of binary data, or a sequence of compression and encoding methods, are the ways data is compressed and/or eventually encoded to decrease its volume (and eventually be exchanged in text format). They imply the way compressed/encoded data should be decompressed/decoded to be readable in its original form again. http://wsio.org continuant snap:Continuant Data compression and encoding http://wsio.org Data compression and/or encoding method http://wsio.org However, one should note that 'Compression and encoding' is not limited only to explicit compression, encoding, or combined methods or algorithms. Form of data compression and/or encoding http://wsio.org Type of data compression and/or encoding http://wsio.org Compressed and/or encoded data format http://wsio.org The same concept in the case when 'Compression and encoding' is used in a role of semantically annotating data entities. Format http://edamontology.org/format_1915 A broader concept in the case when the 'Compression' sub-ontology is used in a role of semantically annotating data entities. Narrower in the sense of being limited to data format. Operation http://wsio.org/operation_001 Form of data compression and/or encoding is related to operations of compressing, decompressing, encoding, and decoding data. Process http://wsio.org Form of data compression and/or encoding is related to processes of compressing, decompressing, encoding, and decoding data. function snap:Function Form of data compression and/or encoding is related to functions of compressing, decompressing, encoding, and decoding data. process span:Process Form of data compression and/or encoding is related to processes of compressing, decompressing, encoding, and decoding data. quality snap:Quality BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the form of data compression and/or encoding. Data compression (form of data compression) is the way data is compressed to decrease its volume, and the implied way how it should be decompressed to be readable in its original form again. It may include archiving of multiple files. Data compression method Form of data compression Type of data compression Compressed data format WSIO Binary format WSIO_compression:014 Data compression WSIO:compression:014 Data compression (form of data compression) is the way data is compressed to decrease its volume, and the implied way how it should be decompressed to be readable in its original form again. It may include archiving of multiple files. http://wsio.org Data compression method http://wsio.org However, one should note that 'Data compression' is not limited only to an explicit compression method and not to an explicit compression algorithm. Form of data compression http://wsio.org Type of data compression http://wsio.org Compressed data format http://wsio.org The same concept in the case when 'Data compression' is used in a role of semantically annotating data entities. Binary format http://edamontology.org/format_2333 Typically, but not necessarily, the format of compressed data is binary. Applies when 'Data compression' is used in a role of semantically annotating compressed data entities. Data compression (type of data compression), an encoding method of binary data, or a sequence of compression and encoding methods, are the ways data is compressed and/or eventually encoded. Data compression method Form of data compression Type of data compression Binary-to-text encoded format WSIO Text format WSIO_compression:015 Binary-to-text encoding WSIO:compression:015 Data compression (type of data compression), an encoding method of binary data, or a sequence of compression and encoding methods, are the ways data is compressed and/or eventually encoded. http://wsio.org Data compression method http://wsio.org However, one should note that 'Data compression' is not limited only to an explicit compression method and not to an explicit compression algorithm. Form of data compression http://wsio.org Type of data compression http://wsio.org Binary-to-text encoded format http://wsio.org The same concept in the case when 'Binary-to-text encoding' is used in a role of semantically annotating encoded data entities. Text format http://edamontology.org/format_2330 A broader concept in the case when the 'Binary-to-text encoding' is used in a role of semantically annotating encoded data entities. Narrower in the sense of being limited to data format. Combination of forms of data compression and/or binary-to-text encoding is a sequence of data compressions and encodings that decreases the data volume and encodes it in the desired format. The reverse sequence of compressions and encodings should be used to decompress and decode the data into its original form. Combined data compression and encoding method Sequence of forms of data compression and binary-to-text encoding Compressed and encoded data format WSIO WSIO_compression:016 In the specialised ontology concepts of 'Combination of compression and encoding', the forms of compression and encoding are listed in their names (terms) in the order of the compression/encoding sequence. The reverse sequence must be used for decompression/decoding. Combination of compression and encoding WSIO:compression:016 Combination of forms of data compression and/or binary-to-text encoding is a sequence of data compressions and encodings that decreases the data volume and encodes it in the desired format. The reverse sequence of compressions and encodings should be used to decompress and decode the data into its original form. http://wsio.org Combined data compression and encoding method http://wsio.org However, one should note that 'Combination of compression and encoding' is not limited only to explicit combined methods or algorithms. Sequence of forms of data compression and binary-to-text encoding http://wsio.org Compressed and encoded data format http://wsio.org The same concept in the case when 'Combination of compression and encoding' is used in a role of semantically annotating compressed and encoded data entities. ZIP is a compressed and archived data format, and a compression and archiving method, supported by multiple tools and systems. Binary format http://en.wikipedia.org/wiki/ZIP_file_format WSIO WSIO_compression:017 ZIP WSIO:compression:017 ZIP is a compressed and archived data format, and a compression and archiving method, supported by multiple tools and systems. http://wsio.org Binary format http://edamontology.org/format_2333 gzip (GNU zip) is a compression method supported by multiple tools and systems. It has a corresponding gzip data format. http://en.wikipedia.org/wiki/Gzip WSIO WSIO_compression:018 gzip WSIO:compression:018 gzip (GNU zip) is a compression method supported by multiple tools and systems. It has a corresponding gzip data format. http://wsio.org tar archive (tape archive) compressed by gzip. WSIO gzip tar (file format) WSIO_compression:019 tar gzip WSIO:compression:019 tar (file format) http://en.wikipedia.org/wiki/Tar_(file_format) tar archive (tape archive) compressed by gzip. http://wsio.org gzip http://en.wikipedia.org/wiki/Gzip Efficient XML Interchange (EXI) is a compressed binary data format and a form of compression of XML-formatted data. http://www.w3.org/TR/exi WSIO WSIO_compression:020 EXI WSIO:compression:020 Efficient XML Interchange (EXI) is a compressed binary data format and a form of compression of XML-formatted data. http://wsio.org base64 is a form of representing binary data in text format. http://en.wikipedia.org/wiki/Base64 WSIO WSIO_compression:021 base64 WSIO:compression:021 base64 is a form of representing binary data in text format. http://wsio.org 'gzip base64' combines compression by gzip followed by base64 encoding. WSIO WSIO_compression:022 gzip base64 WSIO:compression:022 'gzip base64' combines compression by gzip followed by base64 encoding. http://wsio.org 7z is a compressed data format supporting multiple algorithms. WSIO WSIO_compression:031 7z WSIO:compression:031 7z is a compressed data format supporting multiple algorithms. http://wsio.org Data is an information artefact that is 'understandable' by dedicated computational tools that can use the data as input or produce as output. continuant http://edamontology.org/data_0006 WSIO data item information content entity WSIO_data:002 A top-level concept in WSIO rooting the 'Data' sub-ontology. WSIO 'Data' sub-ontology includes types of data that are relevant with respect to interaction scenarios with Web services, including session handling (for example 'explicit polling' within asynchronous invocation). Concepts of WSIO 'Data' sub-ontology are applicable also outside of the context of Web-service interaction. Data WSIO:data:002 Data is an information artefact that is 'understandable' by dedicated computational tools that can use the data as input or produce as output. http://wsio.org continuant snap:Continuant data item http://purl.obolibrary.org/obo/IAO_0000027 IAO 'data item' is a closely related ontological category (concept) broader in the sense of being any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant), standing in relation of aboutness to some entity (http://purl.obolibrary.org/obo/IAO_0000030), and to data that is intended to be a truthful statement about something. information content entity http://purl.obolibrary.org/obo/IAO_0000030 IAO 'information content entity' is a closely related ontological category (concept) broader in the sense of covering any type of data in any role, and narrower in the sense of being limited to a 'generically_dependent_continuant' (snap:GenericallyDependentContinuant) and standing in relation of aboutness to some entity. Identifier is a datum uniquely identifying an entity. http://edamontology.org/data_0842 ID WSIO WSIO_data:005 Identifier WSIO:data:005 Identifier is a datum uniquely identifying an entity. http://wsio.org ID http://wsio.org Computation ID is a unique identifier of a computation process instance, that is used by the infrastructure responsible for the computation. Computation ID WSIO WSIO_data:009 Job ID WSIO:data:009 Computation ID is a unique identifier of a computation process instance, that is used by the infrastructure responsible for the computation. http://wsio.org Computation ID http://wsio.org Session status is a datum describing a state of a session. Computation status Job status Session status WSIO WSIO_data:010 Status WSIO:data:010 Session status is a datum describing a state of a session. http://wsio.org Computation status http://wsio.org Job status http://wsio.org Session status http://wsio.org Result is a datum (output argument) holding the result of a computation, or the actual (full, partial, or a part of) resulting data of a computation. Computation result WSIO WSIO_data:026 Result WSIO:data:026 Result is a datum (output argument) holding the result of a computation, or the actual (full, partial, or a part of) resulting data of a computation. http://wsio.org Computation result http://wsio.org TODO. WSIO WSIO_data:027 Job in progress WSIO:data:027 TODO. http://wsio.org TODO. WSIO WSIO_data:028 Job completed WSIO:data:028 TODO. http://wsio.org TODO. WSIO WSIO_data:029 Job aborted WSIO:data:029 TODO. http://wsio.org TODO. WSIO WSIO_data:030 Job progress (in percent) WSIO:data:030 TODO. http://wsio.org Operation is a function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). Function continuant http://edamontology.org/operation_0004 Computational method Computational operation Computational procedure Computational subroutine Function (mathematics) Function (programming) Lambda abstraction Mathematical function Mathematical operation Subroutine WSIO Process function process quality WSIO_operation:001 A singular case is a constant operation (constant function) that consumes no input (has no input arguments). A top-level concept in WSIO rooting the 'Operation' sub-ontology. WSIO 'Operation' sub-ontology includes operations that are relevant with respect to interaction scenarios with Web services, including session handling (for example 'explicit polling' within asynchronous invocation). Some concepts of WSIO 'Operation' sub-ontology are applicable also outside of the context of Web-service interaction. Operation WSIO:operation:001 Operation is a function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). http://wsio.org Function http://wsio.org Operation is a function that has input(s) and output(s). continuant snap:Continuant Computational method http://wsio.org Computational operation http://wsio.org Computational procedure http://wsio.org Computational subroutine http://wsio.org Function (mathematics) http://en.wikipedia.org/wiki/Function_(mathematics) Function (programming) http://wsio.org Lambda abstraction http://wsio.org Mathematical function http://wsio.org Mathematical operation http://wsio.org Subroutine http://en.wikipedia.org/wiki/Function_(computer_science) http://en.wikipedia.org/wiki/Subroutine Process http://wsio.org Process can have a function (as its quality/attribute), and can also have (perform) an 'Operation' with inputs and outputs. function snap:Function BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s). process span:Process Process can have a function (as its quality/attribute), and can also have (perform) an 'Operation' with inputs and outputs. quality snap:Quality Function, including an operation, can have a role of a quality/attribute in semantic annotation. 'Submit job' is an operation that submits a new computational task. Job submission WSIO WSIO_operation:006 Job submission WSIO:operation:006 'Submit job' is an operation that submits a new computational task. http://wsio.org Job submission http://wsio.org 'Get status' is an operation that returns a status of a session or a computation. Get session status Query status Get computation status Get job status WSIO WSIO_operation:007 Status retrieval WSIO:operation:007 'Get status' is an operation that returns a status of a session or a computation. http://wsio.org Get session status http://wsio.org Query status http://wsio.org Get computation status http://wsio.org Get job status http://wsio.org 'Get result' is an operation that returns a result of a computation. Fetch result Get results WSIO WSIO_operation:008 Result retrieval WSIO:operation:008 'Get result' is an operation that returns a result of a computation. http://wsio.org Fetch result http://wsio.org Get results http://wsio.org 'Init session' is an operation that starts a new session. Open session Start new session WSIO WSIO_operation:023 Init session WSIO:operation:023 'Init session' is an operation that starts a new session. http://wsio.org Open session http://wsio.org Start new session http://wsio.org 'Send data' is an operation that sends or sets the payload input data for a computation. Send input Send payload input data Set data WSIO WSIO_operation:024 Send data WSIO:operation:024 'Send data' is an operation that sends or sets the payload input data for a computation. http://wsio.org Send input http://wsio.org Send payload input data http://wsio.org Set data http://wsio.org 'Set parameters' is an operation that sets the (input) parameters of a parameterised computation. Send input Send parameters WSIO WSIO_operation:025 Set parameters WSIO:operation:025 'Set parameters' is an operation that sets the (input) parameters of a parameterised computation. http://wsio.org Send input http://wsio.org Send parameters http://wsio.org Transfer (type of data transfer, data transfer protocol) is the way data is transfered between 2 locations or processes. continuant Data channel Data transfer Data transfer protocol Form of data transfer Type of data transfer WSIO Function Process function process quality WSIO_transfer:003 Types of transfer are not bound to any particular layer of the OSI Model (http://en.wikipedia.org/wiki/OSI_model). A top-level concept in WSIO rooting the 'Transfer' sub-ontology. WSIO 'Transfer' sub-ontology includes forms of transfer and transfer protocols that are relevant with respect to transferring input and output data to and from Web services. Some concepts of WSIO 'Transfer' sub-ontology are applicable also outside of the context of Web-service interaction. Transfer WSIO:transfer:003 Transfer (type of data transfer, data transfer protocol) is the way data is transfered between 2 locations or processes. http://wsio.org continuant snap:Continuant Data channel http://wsio.org Data transfer http://wsio.org Data transfer protocol http://wsio.org Form of data transfer http://wsio.org Type of data transfer http://wsio.org Function http://wsio.org Form of data transfer is related to a function of transferring data. Process http://wsio.org Form of data transfer is related to a process of transferring data. function snap:Function Form of data transfer is related to a function of transferring data. process span:Process Form of data transfer is related to a process of transferring data. quality snap:Quality BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the form of data transfer. 'In SOAP body' is a form of data transfer inside the body of a SOAP message. In-line SOAP WSIO WSIO_transfer:011 In SOAP body WSIO:transfer:011 'In SOAP body' is a form of data transfer inside the body of a SOAP message. http://wsio.org In-line http://wsio.org SOAP http://wsio.org MTOM is a form of data transfer as an MTOM attachment of a SOAP message. WSIO WSIO_transfer:012 MTOM WSIO:transfer:012 MTOM is a form of data transfer as an MTOM attachment of a SOAP message. http://wsio.org 'Download from URL' is a form of data transfer by downloading from a specified URL. WSIO WSIO_transfer:013 Within the semantic annotation of forms of transfer of Web services or other tools, the data (argument) holding the specified URL should be annotated as having transfer 'Download from URL'. Download from URL WSIO:transfer:013 'Download from URL' is a form of data transfer by downloading from a specified URL. http://wsio.org 19:06:2014 23:03 WSIO WSIO 1.2 032 Matus Kalas Acknowledgement for technical support: Torbjorn Lium, Lorand Janos Szentennai, Stanislav Oltu. Author: Matus Kalas, (c) 2011-2014, Computational Biology Unit, Department of Informatics, University of Bergen, Norway. Licence: Available under the Creative Commons BY-ND 3.0 licence with allowed attributed reference to, and import of, unmodified( PIs: Inge Jonassen, Kjell Petersen, Ibid. Web Service Interaction Ontology (WSIO) enables automated interaction with more complex Web services that are typical for example within life sciences. WSIO is however independent of the application domain and relevant for both SOAP and REST Web services, and for batch execution engines in general. If the interaction scenario with a Web service is nontrivial (and incorporates session handling), annotation with WSIO concepts will enable automatic generation of client programs, scripts, or interactive applications with a graphical user interface. WSIO also enables automation of different ways of data transfer and data un-/compression or en-/decoding. We strongly discourage providers from developing complex interaction and data-transfer/compression scenarios, however when needed, WSIO may enable smooth automated interaction with them. Future versions will support more interaction scenarios. WSIO aims to serve also as a means to standardise the complex interaction scenarios primarily within both SOAP and REST Web services, and secondarily to apply also to batch execution infrastructure in general. beta2