README formatting and typo.
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David Arndt
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README.md
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README.md
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[**ClassyFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. This is the repository for the ClassyFire API allows you to send requests to and pull information from the ClassyFire web server.
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[**ClassyFire**](http://classyfire.wishartlab.com) is a resource that allows you to automatically classify any chemical compound based on its structure. This is the repository for the ClassyFire API, which allows you to send requests to and pull information from the ClassyFire web server.
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# **Endpoints** #
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# **Endpoints** #
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> ##1. Entity##
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##1. Entity##
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>
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> >Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification.
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Chemical compounds are represented by the Entity model, through which one can access the compound's structure-based classification.
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> >
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> >###GET###
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###GET###
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> >
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> >**/entities/{entityInchikey}**
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**/entities/{entityInchikey}**
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> >
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> >A chemical compound's classification can be retrieved in the JSON or XML format. The compound's information is accessed via the InChIkey as show in the following examples. In this example, the entity has the InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.
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A chemical compound's classification can be retrieved in the JSON or XML format. The compound's information is accessed via the InChIkey as show in the following examples. In this example, the entity has the InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.
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> > >
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> > >ClassyFireAPI.get_entity_classification("BDAGIHXWWSANSR-UHFFFAOYSA-N","json")
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ClassyFireAPI.get_entity_classification("BDAGIHXWWSANSR-UHFFFAOYSA-N","json")
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> >
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> > Where:
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Where:
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> >
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> > >The entity's InChIKey is "BDAGIHXWWSANSR-UHFFFAOYSA-N",
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* The entity's InChIKey is "BDAGIHXWWSANSR-UHFFFAOYSA-N",
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> > >
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* The output format is "json" (JSON).
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> > >The output format is "json" (JSON).
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##2. Sequence##
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> ##2. Sequence##
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>
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Sequences are represented by the Sequence model, through which one can access the compound's structure-based classification.
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> >Sequences are represented by the Sequence model, through which one can access the compound's structure-based classification.
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> >
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###GET###
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> >###GET###
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> >
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**/sequence/{fingerprint}**
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> >**/sequence/{fingerprint}**
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> >
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A (FASTA) sequence's classification can be retrieved in the JSON. In this example, the sequence has the fingerprint = "8bf70c23ac100cd2c3955081d8613325"
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> >A (FASTA) sequence's classification can be retrieved in the JSON. In this example, the sequence has the fingerprint = "8bf70c23ac100cd2c3955081d8613325"
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> > >
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ClassyFireAPI.get_sequence_classification("8bf70c23ac100cd2c3955081d8613325","json")
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> > >ClassyFireAPI.get_sequence_classification("8bf70c23ac100cd2c3955081d8613325","json")
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> >
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Where:
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> > Where:
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> >
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* The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325",
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> > >The sequence's fingerprint is "8bf70c23ac100cd2c3955081d8613325",
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* The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS"
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> > > > The fingerprint is generate by Digest::MD5 from the peptide sequence "APDVQDCPECTLQENPFFSQPGAPILQCMGCCFSRAYPTPLRSKKTMLVQKNVTSESTCCVAKSYNRVTVMGGFKVENHTACHCSTCYYHKS"
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* The output format is "json" (JSON).
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> > >
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> > >The output format is "json" (JSON).
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##3. Query##
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> ##3. Query##
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The Query model represents the chemical structure to be classified. Its attributes are the query label and the query input.
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>
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The query label is an identifier
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> >The Query model represents the chemical structure to be classified. Its attributes are the query label and the query input.
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> > >The query label is an identifier
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The query input contains the compound's identifier (optional) and its structural representation, separated by a tab. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) format, the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Moreover, the compound can be represented with its [IUPAC name](http://www.chem.qmul.ac.uk/iupac/).
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> > >
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The input can also be of type [FASTA](https://en.wikipedia.org/wiki/FASTA_format), which contains peptide or nucleotide sequences.
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> > >The query input contains the compound's identifier (optional) and its structural representation, separated by a tab. The chemical structure is represented either in the [Daylight SMILES](http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) format, the [InChI](http://www.iupac.org/home/publications/e-resources/inchi.html) format. Moreover, the compound can be represented with its [IUPAC name](http://www.chem.qmul.ac.uk/iupac/).
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> > >The input can also be of type [FASTA](https://en.wikipedia.org/wiki/FASTA_format), which contains peptide or nucleotide sequences.
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###POST###
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> >
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A query can be submitted using the POST method as demonstrated in the following example.
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> >###POST###
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> >A query can be submitted using the POST method as demonstrated in the following example.
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ClassyFireAPI.submit_query("curl_test","MOL1\\tCCCOCC\\nMOL2\\tCOCC=CCCC","STRUCTURE")
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> > >ClassyFireAPI.submit_query("curl_test","MOL1\\tCCCOCC\\nMOL2\\tCOCC=CCCC","STRUCTURE")
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> >where the parameters are:
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where the parameters are:
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> >
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> > >The query label: curl_test,
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* The query label: curl_test,
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> > >
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* The entity identifiers: MOL1,MOL2
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> > >The entity identifiers: MOL1,MOL2
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* The entity's structure represented in the SMILES format: CCCOCC and COCC=CCCC.
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> >
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* The query is of type 'STRUCTURE'
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> > >The entity's structure represented in the SMILES format: CCCOCC and COCC=CCCC.
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> >
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###GET###
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> > >The query is of type 'STRUCTURE'
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**/queries/{queryId}**
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> >###GET###
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> >
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The classification results can be retrieved via a GET method in the JSON or XML format.
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> >**/queries/{queryId}**
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> >
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ClassyFireAPI.get_query(443431,"json")
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> >The classification results can be retrieved via a GET method in the JSON or XML format.
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> > >
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where:
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> > >ClassyFireAPI.get_query(443431,"json")
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> >
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* The query id is 443431,
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> >where:
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* The output format is "json" (JSON)
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> > >The query id is 443431,
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> > >The output format is "json" (JSON)
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# **Help and Feedback** #
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# **Directory Structure** #
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Feel free to send us any questions of feedback [here](http://feedback.wishartlab.com/?site=classyfire).
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* lib
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# **Who do I talk to?** #
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* Yannick Djoumbou Feunang: djoumbou@ualberta.ca
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* Other community or team contact
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