BioCyc Web Services

TEST

• Data retrieval services that return data in XML, JSON, and/or column-delimited formats (BioCyc data can also be downloaded in a variety of XML and non-XML formats)

• Visualization services, e.g., to map gene expression data onto pathway diagrams

• Services for manipulating SmartTables

Note that in order to access BioCyc web services you must establish a session (see below) and utilize the returned cookies in subsequent web-services calls.

Establishing a Web Services session

To use the BioCyc web services, you must establish a session and log in to your BioCyc account by POSTing your email and password to https://websvc.biocyc.org/credentials/login/. The cookies returned from this request must then be passed back to BioCyc for every subsequent web service request.

Example using curl

    # Log in and save cookies to file biocyc_cookies (POST only):
    curl -c biocyc_cookies -d "email=[email]&password=[password]" -X POST https://websvc.biocyc.org/credentials/login/
    # Issue web service request, passing cookie file:
    curl -b biocyc_cookies https://websvc.biocyc.org/[request]
  

Example using python Requests module

    s = requests.Session() # create session
    # Post login credentials to session:
    s.post('https://websvc.biocyc.org/credentials/login/', data={'email':'[email]', 'password':'[password]'})
    # Issue web service request:
    r = s.get('https://websvc.biocyc.org/[request]')
  

Data Retrieval Web Services: Pathway Tools XML

The following documents will be useful in interpreting the ptools-xml format:

Retrieve a Single BioCyc Object

Biocyc KB-Version Retrieval

The URLs for retrieving the KB-version is

https://websvc.biocyc.org/kb-version?orgid=[ORGID]

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, BSUB.

Example URLs:

• https://websvc.biocyc.org/kb-version?orgid=ECOLI

The default output is a JSON format as follows:

{"kb-version":"19.5"}

Biocyc Object-Id-Based Retrieval of XML Data

The URL to retrieve a single BioCyc object in ptools-xml format is

https://websvc.biocyc.org/getxml?[ORGID]:[OBJECT-ID] or
https://websvc.biocyc.org/getxml?id=[ORGID]:[OBJECT-id]&detail=[none|low|full]

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [OBJECT-ID] is in the BioCyc identifier for the object, e.g. ARGSYN-PWY, EG11025, FRUCTOSE-6P. Note that object identifiers are case-sensitive.
• [none|low|full] indicates whether the returned output should contain no detail, low detail or full detail for the requested object. If no detail parameter is supplied, the request defaults to full detail.

Example URLs:

• https://websvc.biocyc.org/getxml?BSUB:GLYCOLYSIS
  Retrieve the glycolysis pathway in Bacillus subtilis in ptools-xml format.
• https://websvc.biocyc.org/getxml?id=META:ASPARTATEKIN-RXN
  Retrieve the aspartate kinase reaction from MetaCyc in ptools-xml format.
• https://websvc.biocyc.org/getxml?id=ECOLI:TRYPSYN-APROTEIN&detail=low
  Retrieve the trpA gene product from EcoCyc at low detail level.

Search and Retrieve a Set of Objects

Retrieving a Set of Objects Using the Pathway Tools API Functions

The set of Pathway Tools API functions were defined to allow users who have downloaded and installed the Pathway Tools software locally (why do this?) to write programs that operate on the data. A subset of these API functions have been made available via the web services interface.

The URL to issue an API query that returns a list of objects in ptools-xml format is

https://websvc.biocyc.org/apixml?fn=[API-FUNCTION]&id=[ORGID]:[OBJECT-ID]&detail=[none|low|full]

where [ORGID], [OBJECT-ID] and detail level are as for the single object queries described above, and [API-FUNCTION] is one of the following:

• all-products-of-gene
• binding-site-transcription-factors
• chromosome-of-gene
• compounds-of-pathway
• containers-of
• containing-tus
• direct-activators
• direct-inhibitors
• enzymes-of-gene
• enzymes-of-pathway
• enzymes-of-reaction
• genes-of-pathway
• genes-of-protein
• genes-of-reaction
• genes-regulated-by-gene
• genes-regulating-gene
• get-class-all-instances
• get-class-all-subs
• get-class-direct-supers
• get-class-direct-subs
• modified-containers
• modified-forms
• monomers-of-protein
• pathways-of-compound
• pathways-of-gene
• reactions-of-compound
• reactions-of-enzyme
• reactions-of-gene
• regulator-proteins-of-transcription-unit
• regulon-of-protein
• substrates-of-reaction
• top-containers
• transcription-unit-activators
• transcription-unit-binding-sites
• transcription-unit-genes
• transcription-unit-inhibitors
• transcription-unit-mrna-binding-sites
• transcription-unit-promoter
• transcription-unit-terminators
• transcription-unit-transcription-factors
• transcription-units-of-gene
• transcription-units-of-protein

A more detailed description of each API function is available here.

Example URLs:

• https://websvc.biocyc.org/apixml?fn=genes-of-pathway&id=BSUB:GLYCOLYSIS
  Retrieve the set of genes that participate in the glycolysis pathway in Bacillus subtilis.
• https://websvc.biocyc.org/apixml?fn=genes-regulated-by-gene&id=ECOLI:EG10164&detail=none
  Retrieve the set of genes (IDs only) regulated by the crp gene in EcoCyc.
• https://websvc.biocyc.org/apixml?fn=enzymes-of-reaction&id=META:TRYPSYN-RXN&detail=full
  Get detailed information on all enzymes in MetaCyc that catalyze the tryptophan synthase reaction.
• https://websvc.biocyc.org/apixml?fn=get-class-all-instances&id=META:Genes&detail=full
  Get detailed information on all genes in MetaCyc.

Retrieving the Set of Objects Returned by a BioVelo Query

The URL to issue a BioVelo query that returns a list of objects in ptools-xml format is

https://websvc.biocyc.org/xmlquery?[QUERY] or
https://websvc.biocyc.org/xmlquery?query=[QUERY]&detail=[none|low|full]

where

• [QUERY] is a properly escaped BioVelo query string that returns a single list of Pathway Tools objects (it is possible to create BioVelo queries that return multi-column tables -- these are not appropriate as input for this web service). For more information about constructing BioVelo queries, see the Guide to the BioVelo Query Language.
• [none|low|full] indicates whether the returned output should contain no detail (i.e. only object identifiers and links will be included), low detail (names and a handful of other attributes will be included) or full detail for the matching objects. If no detail parameter is supplied, the request defaults to low detail.

NOTE: the BioVelo query needs to be URL encoded if it contains any non-alphanumeric characters. You might look here, or here if you are unfamiliar with URL encoding.

Example URLs:

• https://websvc.biocyc.org/xmlquery?%5bx%3ax%3c-ecoli%5e%5epathways%5d
  Retrieve the complete set of pathways in the EcoCyc database at low detail, where the query [x:x<-ecoli^^pathways]
  has been URL encoded as %5bx%3ax%3c-ecoli%5e%5epathways%5d.
• https://websvc.biocyc.org/xmlquery?query=[x:x<-ecoli^^genes,x^name%3D"trpA"]&detail=full
  Retrieve the gene (or genes) in the EcoCyc database with the name "trpA" in full detail,
  where the query [x:x<-ecoli^^genes,x^name%3D"trpA"]
  has been encoded as %5bx%3ax%3c-ecoli%5e%5egenes%2cx%5ename%253D%22trpA%22%5d.
• https://websvc.biocyc.org/xmlquery?dbs
  Retrieve the set of available organism databases, and the query requires no URL encoding.
• https://websvc.biocyc.org/xmlquery?%5bx%3ay%3a%3dbsub~argsynbsub-pwy%2cx%3c-(enzymes-of-pathway+y)%5d
  Retrieve the set of enzymes that participate in the arginine biosynthesis pathway in Bacillus subtilis,
  where the query [x:y:=bsub~argsynbsub-pwy,x<-(enzymes-of-pathway y)]
  has been URL encoded as %5bx%3ay%3a%3dbsub~argsynbsub-pwy%2cx%3c-(enzymes-of-pathway+y)%5d.
• https://websvc.biocyc.org/xmlquery?%5bx%3ax%3c-meta%5e%5eproteins%2c+%22aspartate%22+instringci+x%5enames%26%22kinase%22+instringci+x%5enames%5d
  Retrieve the set of proteins in MetaCyc that have the words "aspartate" and "kinase" in their common-name or synonyms
  where the query [x:x<-meta^^proteins, "aspartate" instringci x^names&"kinase" instringci x^names]
  has been URL encoded as %5bx%3ax%3c-meta%5e%5eproteins%2c+%22aspartate%22+instringci+x%5enames%26%22kinase%22+instringci+x%5enames%5d.
• https://websvc.biocyc.org/xmlquery?query=%5bx%3ax%3c-ecoli%5e%5epathways%2cecoli~EG10258+in+(pathway-to-genes+x)%5d&detail=none
  Retrieve the identifiers of all pathways containing the eno (enolase) gene in Escherichia coli,
  where the query [x:x<-ecoli^^pathways,ecoli~EG10258 in (pathway-to-genes x)]
  has been encoded as %5bx%3ax%3c-ecoli%5e%5epathways%2cecoli~EG10258+in+(pathway-to-genes+x)%5d.

Data Retrieval Web Services: BioPAX XML

https://websvc.biocyc.org/[ORGID]/pathway-biopax?type=[2|3]&object=[PATHWAY]

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159
• [2|3] specifies whether data should use BioPAX Level 2 or Level 3. If the type argument is omitted, BioPAX Level 3 will be generated.
• [PATHWAY] is in the BioCyc identifier for the pathway, e.g. GLYCOLYSIS, ARGSYN-PWY, PWY0-1299

Example URLs:

• https://websvc.biocyc.org/BSUB/pathway-biopax?type=3&object=GLYCOLYSIS
  Retrieve the glycolysis pathway in Bacillus subtilis in BioPAX Level 3 format.
• https://websvc.biocyc.org/AFER243159/pathway-biopax?type=2&object=CYSTSYN-PWY
  Retrieve the cysteine biosynthesis pathway in Acidithiobacillus ferrooxidans in BioPAX Level 2 format.
• https://websvc.biocyc.org/META/pathway-biopax?object=PWY-5025
  Retrieve the IAA biosynthesis pathway in MetaCyc in BioPAX Level 3 format.

Retrieving a BioCyc Object Given a Foreign ID

BioCyc objects such as pathways, reactions, compounds, genes, proteins, RNAs, or transcription-units in a PGDB can be retrieved given a foreign identifier that matches that object.

The URLs to search for objects based on foreign identifier are

https://websvc.biocyc.org/[ORGID]/foreignid?ids=[DATABASE-NAME]:[FOREIGNID] or
https://websvc.biocyc.org/[ORGID]/foreignid?ids=[DATABASE-NAME]:[FOREIGNID]&fmt=json

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [DATABASE-NAME] is the name of external database, e.g. KEGG, PUBCHEM, UNIPROT.
• [FOREIGNID] is the external database identifier. The foreignid input may contain one or more values, which may be separated by commas. Note that foreignids are case-sensitive.
• fmt=json requests output in the JSON format; default output is in tab-delimited format.

Example URLs:

• https://websvc.biocyc.org/META/foreignid?ids=Kegg:C00849
  Retrieve the object that contains a KEGG link of C00849 in MetaCyc.
• https://websvc.biocyc.org/ECOLI/foreignid?ids=Kegg:C00849,EcoGene:EG11025
  Retrieve objects in EcoCyc that contain a KEGG link of C00849 or an EcoGene link of EG11025.
• https://websvc.biocyc.org/BSUB/foreignid?ids=UniProt:P05653&fmt=json
  Retrieve the object that contains a UniProt link of P05653 in Bacillus subtilis in JSON format.

The default output is a tab-delimited format as follows:

Kegg:C00849	1	ETHYLACETATE
EcoGene:EG11025	1	EG11025

where

column 1 : Input Foreign ID.
column 2 : 1 means that a valid object that matches the foreign ID was found and 0 means that no object that matches the foreign ID was found.
column 3 : The BioCyc identifier of the object that matches the foreign ID.

JSON format:

[{"INPUT":"UniProt:P05653","STATUS":1,"RESULTS":[{"ID":"BSU00070-MONOMER"}]}]

Retrieving a BioCyc Object Given a Chemical Formula

The URLs to search metabolites based on chemical formula are

https://websvc.biocyc.org/[ORGID]/CF?cfs=[CHEMICAL-FORMULA] or
https://websvc.biocyc.org/[ORGID]/CF?cfs=[CHEMICAL-FORMULA]&fmt=json

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [CHEMICAL-FORMULA] is the chemical formula to be matched, in the format ([element-symbol][coefficient])+. The chemical formula input may contain one or more values, which may be separated by commas. The search will return all metabolites in the specified database that have the exact chemical formula(s) provided here.
• fmt=json requests output in JSON format; default output is in tab-delimited format

Example URLs:

• https://websvc.biocyc.org/META/CF?cfs=C6H6
  Retrieve the compound that contains a chemical formula of C6H6 in MetaCyc.
• https://websvc.biocyc.org/ECOLI/CF?cfs=C6H12O6,H2O
  Retrieve the compounds that contain the chemical formulas C6H12O6 and H2O in EcoCyc.
• https://websvc.biocyc.org/BSUB/CF?cfs=C6H6&fmt=json
  Retrieve the compound that contains a Chemical formula of C6H6 in Bacillus subtilis in JSON format.

The default output is a tab-delimited format as follows:

C6H6	1	BENZENE		benzene
H2O3	0

where

column 1 : Input Chemical Formula.
column 2 : 1 means that a valid compound that matches the chemical formula was found; 0 means that no match was found.
column 3 : The BioCyc identifier of the compound that matches the chemical formula.
column 4 : The common-name of the compound.

JSON format:

[{"INPUT":"H2O2","STATUS":1,"RESULTS":[{"ID":"HYDROGEN-PEROXIDE","NAME":"hydrogen peroxide"}]},{"INPUT":"H2O3","STATUS":0}]

Retrieving a BioCyc Compound given a Monoisotopic Weight and Tolerance

The URLs to search for compounds based on monoisotopic molecular weight and tolerance are

https://websvc.biocyc.org/[ORGID]/monoisotopicwt?wts=[MONOISOTOPICMW]&tol=[TOLERANCE] or
https://websvc.biocyc.org/[ORGID]/monoisotopicwt?wts=[MONOISOTOPICMW]&tol=[TOLERANCE]&fmt=json

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [MONOISOTOPICMW] is a floating point number, standing for the monoisotopic molecular weight in daltons. One or more monoisotopic molecular weights can be supplied, where multiple values are separated by commas.
• [TOLERANCE] is the search tolerance +/- in ppm.
• fmt=json requests output in the JSON format; default output is in tab-delimited format

Example URLs:

• https://websvc.biocyc.org//META/monoisotopicwt?wts=123.009&tol=5
  Retrieve the compounds that have a monoisotopic molecular weight of 123.009 and tolerance of 5 in MetaCyc.
• https://websvc.biocyc.org/ECOLI/monoisotopicwt?wts=240.063,88.052&tol=5
  Retrieve the compounds that have a monoisotopic molecular weight of either 240.063 or 88.052 and tolerance of 5 in EcoCyc.
• https://websvc.biocyc.org/BSUB/monoisotopicwt?wts=169.988&tol=5&fmt=JSON
  Retrieve the compounds that have a monoisotopic molecular weight of 169.988 and tolerance of 5 in Bacillus subtilis in JSON format.

The default output is a tab-delimited format as follows:

123.009	1	123.008705	3-chloro-L-alanine	CHLORALAN-CPD
123.009	1	123.008705	3-chloro-D-alanine	3-CHLORO-D-ALANINE
123.009	1	123.008705	2-chloro-L-alanine	CPD0-1475
123.009	1	123.008705	3-chloro-DL-alanine	3-CHLORO-DL-ALANINE
56	0			

where

column 1 : Input monoisotopic molecular weight for this search.
column 2 : 1 means the query was successful and 0 means the query found no match.
column 3 : Monoisotopic molecular weight of the compound that is stored in the PGDB
column 4 : Compound name
column 5 : The BioCyc identifier of the compound.

JSON format:

[{"INPUT":"123.009","STATUS":1,"RESULTS":[{"MW":123.008705,"NAME":"3-chloro-L-alanine","ID":"CHLORALAN-CPD"},{"MW":123.008705,"NAME":"3-chloro-D-alanine","ID":"3-CHLORO-D-ALANINE"},{"MW":123.008705,"NAME":"2-chloro-L-alanine","ID":"CPD0-1475"},{"MW":123.008705,"NAME":"3-chloro-DL-alanine","ID":"3-CHLORO-DL-ALANINE"}]},{"INPUT":"56","STATUS":0}]

Metabolite Translation Service

1) None of the provided fields is recognized in the specified BioCyc database, in which case "unknown" is returned, along with the unknown input fields.

2) All of the recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula match a single metabolite, in which case "successful" is returned, along with the following tab-separated fields:

• BioCyc ID of matching metabolite
• BioCyc common name of matching metabolite
• Additional identifiers present in BioCyc from other databases for the matching metabolite

3) The recognized names, identifiers, InChI string, InChI key, monoisotopic weight, and chemical formula match more than one metabolite, in which case "ambiguous" is returned, along with the ambiguous fields from the input.

The default input for the file or for pasting data is a tab-delimited format.

Example:

Kegg:C00001	PubChem:125
TRP
ACET

The default output is a tab-delimited format as follows:

ambiguous	BioCyc:WATER		BioCyc:4-HYDROXY-BENZYL-ALCOHOL	
success		BioCyc:TRP	L-tryptophan	MetaboLights:MTBLC57912	HMDB:HMDB00929	IAF1260:33772	ChEBI:57912	PubChem:6923516	KEGG:C00078	CAS:73-22-3
success		BioCyc:ACET	acetate		MetaboLights:MTBLC30089	HMDB:HMDB00042	DrugBank:DB03166	IAF1260:33590	ChemSpider:170	PubChem:175	ChEBI:30089	CAS:64-19-7	KEGG:C00033	CAS:71-50-1

To access the metabolite translation service interactively, click here

Retrieve BioCyc Objects from a Class by Name

https://websvc.biocyc.org/[ORGID]/name-search?object=[NAME]&class=[CLASS] or
https://websvc.biocyc.org/[ORGID]/name-search?object=[NAME]&class=[CLASS]&fmt=json

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [NAME] is is the name of the object to retrieve.
• [CLASS] is the class from which the object is to be retrieved, e.g. Genes.
• fmt=json requests output in the JSON format; default output is in tab-delimited format.

Example URLs:

• https://websvc.biocyc.org//ECO/name-search?object=trpa&class=Genes
  Retrieve Genes called trpA.
• https://websvc.biocyc.org/ECO/name-search?object=trpa&class=Genes&fmt=json
  Retrieve Genes called trpA in JSON format.

The default output is a tab-delimited format as follows. If no results are found then the string EMPTY-RESULT is returned.

EG11024	trpA

where

column 1 : BioCyc Object ID
column 2 : Common Name

JSON format:

{"RESULTS":[{"OBJECT-ID":"EG11024","COMMON-NAME":"trpA"}]}

Retrieve BioCyc Objects by SMILES String

https://websvc.biocyc.org/[ORGID]/smiles-search?smiles=[SMILES]&exact=[EXACT] or
https://websvc.biocyc.org/[ORGID]/smiles-search?smiles=[SMILES]&exact=[EXACT]&fmt=json

where

• [ORGID] is the identifier for the organism database, e.g. ECOLI, META, AFER243159.
• [SMILES] is the SMILES string, e.g. CN, CO.
• [EXACT] is a Boolean, either T (true) or F (false).
• fmt=json requests output in the JSON format; default output is in tab-delimited format.

Example URLs:

• https://websvc.biocyc.org/ECO/smiles-search?smiles=CO&exact=F
  Retrieve compounds containing CO, inexact match.
• https://websvc.biocyc.org/ECO/smiles-search?smiles=CO&exact=F&fmt=json
  Retrieve compounds containing CO, inexact match, using JSON format.

The default output is a tab-delimited format as follows. If no results are found then the string EMPTY-RESULT is returned.

CPD-22525	p-aminophenyl-β-D-glucoside	        C(O)[C@@H]2([C@@H](O)[C@H](O)[C@@H](O)[C@H](OC1(\C=C/C(/N)=C\C=1))O2)
CPD-8122	molybdopterin adenine dinucleotide	C(OP(=O)([O-])OP(OC[C@H]2(O[C@H]1(NC3(/N=C(N)\NC(=O)C(/N[C@H]1C(\S)=C2\[S-])=3))))(=O)[O-])[C@H]6(O[C@@H](N4(C5(\C(\N=C/4)=C(N)/N=C\N=5)))[C@H](O)[C@H](O)6)
... 

where

column 1 : BioCyc Object ID
column 2 : Common Name
column 3 : Complete SMILES string

JSON format:

{"RESULTS":[{"OBJECT-ID":"CPD-22525","COMMON-NAME":"p<\/i>-aminophenyl-β-D-glucoside","SMILES":"C(O)[C@@H]2([C@@H](O)[C@H](O)[C@@H](O)[C@H](OC1(\\C=C\/C(\/N)=C\\C=1))O2)"},{"OBJECT-ID":"CPD-8122","COMMON-NAME":"molybdopterin adenine dinucleotide","SMILES":"C(OP(=O)([O-])OP(OC[C@H]2(O[C@H]1(NC3(\/N=C(N)\\NC(=O)C(\/N[C@H]1C(\\S)=C2\\[S-])=3))))(=O)[O-])[C@H]6(O[C@@H](N4(C5(\\C(\\N=C\/4)=C(N)\/N=C\\N=5)))[C@H](O)[C@H](O)6)"},...]}

Retrieve BioCyc Objects by InChI String

CYTOSINE	cytosine	InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)	(1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8) 1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1 1S/C4H5N3O/c5)

// Short form
{"name": "sample short-form group",
 "description": "sample short-form description",
 "pgdb": "ECOLI",
 "type": "Genes",
 "values": ["trpA", "trpB"]
}

// long form (2 columns)
{"name": "sample long-form group",
 "description": "This is a longer form of JSON used with a SmartTable.",
 "columns": [{"name": "Gene",
                      "type": "Genes"},
                    {"name": "Expression Level"}]
 "rows": [{{"frameid": "EG11204", "pgdb": "ECOLI"},
                 "1.3"}
      {{"frameid": "EG11205", "pgdb": "ECOLI"},
        "-2.2"}]
}

<xs:schema attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xs="http://www.w3.org/2001/XMLSchema">
  <xs:element name="GROUP">
    <xs:complexType>
      <xs:attribute type="xs:string" name="ID"/>
      <xs:attribute type="xs:string" name="NAME"/>
      <xs:sequence>
        <xs:element name="COLUMNS">
          <xs:complexType>
            <xs:sequence>
              <xs:element name="COLUMN" maxOccurs="unbounded" minOccurs="1">
                <xs:complexType>
                  <xs:simpleContent>
                    <xs:extension base="xs:string">
                      <xs:attribute type="xs:string" name="NAME" use="optional"/>
                      <xs:attribute type="xs:string" name="TYPE" use="optional"/>
                    </xs:extension>
                  </xs:simpleContent>
                </xs:complexType>
              </xs:element>
            </xs:sequence>
          </xs:complexType>
        </xs:element>
        <xs:element name="ROWS">
          <xs:complexType>
            <xs:sequence>
              <xs:element name="ROW" maxOccurs="unbounded" minOccurs="0">
                <xs:complexType>
                  <xs:sequence>
                    <xs:element name="CELL" maxOccurs="unbounded" minOccurs="0">
                      <xs:complexType mixed="true">
                        <xs:sequence>
                          <xs:element name="FRAME" maxOccurs="unbounded" minOccurs="0">
                            <xs:complexType>
                              <xs:simpleContent>
                                <xs:extension base="xs:string">
                                  <xs:attribute type="xs:string" name="ID" use="optional"/>
                                  <xs:attribute type="xs:string" name="PGDB" use="optional"/>
                                </xs:extension>
                              </xs:simpleContent>
                            </xs:complexType>
                          </xs:element>
                          <xs:element type="xs:string" name="VALUE" maxOccurs="unbounded" minOccurs="0"/>
                        </xs:sequence>
                      </xs:complexType>
                    </xs:element>
                  </xs:sequence>
                </xs:complexType>
              </xs:element>
            </xs:sequence>
          </xs:complexType>
        </xs:element>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
</xs:schema>

<GROUP ID="biocyc14-2762-3579243971" NAME="Import from snp.txt">

  <COLUMNS>
    <COLUMN NAME="Position" TYPE="NUMBER"/>
    <COLUMN NAME="Gene" TYPE="All-Genes"/>

    <COLUMN
     NAME="Map to Alicyclobacillus acidocaldarius acidocaldarius DSM 446"
     TYPE="All-Genes"/>
    <COLUMN NAME="new column"/>

    <COLUMN NAME="Binding sites upstream of gene" TYPE="DNA-Binding-Sites"/>
  </COLUMNS>

  <ROWS>

    <ROW>
      <CELL><VALUE>10</VALUE></CELL>
      <CELL><FRAME ID="EG11024" PGDB="ECOLI"/></CELL>
      <CELL><FRAME ID="GCIO-1719" PGDB="AACI521098"/></CELL>
      <CELL/>

      <CELL>
        <FRAME ID="BS00206" PGDB="ECOLI"/>
        <FRAME ID="BS0-4061" PGDB="ECOLI"/>
        <FRAME ID="BS0-4062" PGDB="ECOLI"/>
      </CELL>
    </ROW>
  </ROWS>
</GROUP>