All the main functions of bioDBnet can be accessed through SOAP API calls. Below is an explanation of the services offered and examples of required parameters

getInputs: Gets all the input nodes in bioDBnet. The inputs are returned as a string of comma separated values.
Input: none
Output: Type: string, Example: 'Affy ID,Agilent ID,Biocarta Pathway Name,CodeLink ID,..,..,UniProt Entry Name,UniProt Protein Name,UniSTS ID'

getOutputsForInput: Gets all the possible output nodes for a given input node (All outputs accessible by following single or multiple edges in the bioDBnet graph). The outputs are returned as a string of comma separated values.
Input: Name: input, Type: string, Example: 'Gene ID'
Output: Type: string, Example: 'Affy ID,Agilent ID,ApiDB_CryptoDB ID,Biocarta Pathway Name,BioCyc ID,..,..,WormPep Transcript ID,Xenbase ID,ZFIN ID'

getDirectOutptsForInput: Gets all the direct output nodes for a given input node (Outputs reachable by single edge connection in the bioDBnet graph). The outputs are returned as a string of comma separated values.
Input: Name: input, Type: string, Example: 'Ensembl Gene ID'
Output: Type: string, Example: 'Affy ID,Agilent ID,CCDS ID,Chromosomal Location,CodeLink ID,..,..,VEGA Transcript ID,WormPep Protein ID,ZFIN ID'

db2db, dbReport, dbWalk and dbFind operations require complex types as input and return the results as a string with the results for each input identifier returned as tab delimited values in separate lines.

db2db: The web service operation offering the functionality of db2db
Input: Complex type db2dbParams
Output: Type:string

dbAnnot: The web service operation offering the functionality of dbAnnot
Input: Complex type dbAnnotParams
Output: Type:string

dbReport: The web service operation offering the functionality of dbReport. Due to the nature of the web services the dbReport results are returned in the same format as db2db. The only difference between the db2db and dbReport services are that db2db returns results only for the requested output types while dbReport returns results for all possible outputs.
Input: Complex type dbReportParams
Output: Type:string

dbWalk: The web service operation offering the functionality of dbWalk
Input: Complex type dbWalkParams
Output: Type:string

dbFind: The web service operation offering the functionality of dbFind
Input: Complex type dbFindParams
Output: Type:string

dbOrtho: The web service operation offering the functionality of dbOrtho
Input: Complex type dbOrthoParams
Output: Type:string

WSDL definitions for the complex types:

<xsd:complexType name="db2dbParams">
  <xsd:all>
   <xsd:element name="input" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputValues" type="xsd:string"/>
   <xsd:element name="outputs" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

<xsd:complexType name="dbAnnotParams">
  <xsd:all>
   <xsd:element name="annotType" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputValues" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

<xsd:complexType name="dbReportParams">
  <xsd:all>
   <xsd:element name="input" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputValues" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

<xsd:complexType name="dbFindParams">
  <xsd:all>
   <xsd:element name="output" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputValues" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

<xsd:complexType name="dbWalkParams">
  <xsd:all>
   <xsd:element name="dbPath" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputValues" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

<xsd:complexType name="dbOrthoParams">
  <xsd:all>
   <xsd:element name="input" type="xsd:string"/>
   <xsd:element name="output" type="xsd:string"/>
   <xsd:element name="taxonId" type="xsd:string"/>
   <xsd:element name="inputTaxon" type="xsd:string"/>
   <xsd:element name="outputTaxon" type="xsd:string"/>
  </xsd:all>
 </xsd:complexType>

Required elements for the complex types:

Element Name: input
Type:string
Description: Value of the type of identifiers submitted as inputs
Example: 'Ensembl Gene ID'
Required for: db2db, dbReport, dbWalk

Element Name: output
Type:string
Description: Value of the type of identifier expected as results
Example: 'Gene ID'
Required for: dbFind

Element Name: outputs
Type:string
Description: Comma separated values of the type of identifiers expected as results
Example: 'Gene Symbol, Ensembl Protein ID', Required for: db2db

Element Name: inputValues
Type:string
Description: Comma separated values of the input identifiers
Example: 'ENSG00000121410, ENSG00000171428'
Required for: db2db, dbReport, dbFind, dbWalk

Element Name: dbPath
Type:string
Description: The custom path to be followed from the input identifer type to get the required output identifiers
Example: 'Ensembl Gene ID->Gene ID->Homolog - Mouse Gene ID->Ensembl Gene ID'
Required for: dbWalk

Element Name: annotType
Type:string
Description: Annotation types available for the dbAnnot functionality
Example: 'Genes, Drugs'
Required for: dbAnnot

Element Name: inputTaxon
Type:string
Description: The Taxon ID of the input identifiers
Example: '9606'
Required for: dbOrtho

Element Name: outputTaxon
Type:string
Description: The Taxon ID of the output identifiers
Example: '9606'
Required for: dbOrtho

Element Name: taxonId
Type:string
Description: The Taxon ID of the input identifiers
Example: '9606'
Required for: db2db, dbAnnot, dbReport, dbFind, dbWalk

Example results for the different operations:

db2db: 'Ensembl Gene ID\tGene Symbol\tEnsembl Protein ID\nENSG00000121410\tA1BG\tENSP00000394644;ENSP00000263100\nENSG00000171428\tAAC1;NAT1\tENSP00000307218\n'

dbAnnot: 'Input Value\tInput Type\tGene Info\tEnsembl Gene Info\tUniProt Info\tDrugBank Drug Info\tPharmGKB Drug Info\nMYC\tGene Symbol\t4609 [Gene Symbol: MYC] [Locus Tag: ] [Chromosome: 8] [Map Location: 8q24.21] [Description: v-myc avian myelocytomatosis viral oncogene homolog] [Gene Type: protein-coding]\tENSG00000136997 [Biotype: protein_coding] [Chr_Location: 8:127735434-127741434]...\tMYC_HUMAN [Acc: P01106] [Seq_length: 439] [PI: 5.33] [Weight: 48803.55] [Organism: Homo sapiens (Human)] [Definition:....\t-\t-\nCPT1A\tGene Symbol\t1374 [Gene Symbol: CPT1A]...ENSG00000110090 [Biotype: protein_coding] [Chr_Location: 11:68754620-68844410]...CPT1A_HUMAN [Acc: P50416]...\tDB00583 [Name: L-Carnitine] [Brand_names: Carnitor...Parenteral levocarnitine is indicated for the prevention and treatment of carnitine deficiency in patients with end-stage renal disease.]\t-\n'

dbReport: 'Ensembl Gene ID\tAffy ID\tAgilent ID\tApiDB_CryptoDB ID\t.....\tWormPep Transcript ID\tXenbase ID\tZFIN ID\nENSG00000121410\t229819_at [Chip: HT_HG-U133B];11741180_a_at [Chip: HG-U219];229819_at [Chip: U133B];Hs.41997.0.A1_3p_at [Chip: U133_X3P];229819_at [Chip: U133_Plus_2];229819_PM_at [Chip: U133_Plus_PM]\t-\t-\t.....\t-\t-\t-\nENSG00000171428\tHs.155956.0.S1_3p_at [Chip: U133_X3P];214440_at [Chip: U133A_2];214440_at [Chip: U133_Plus_2];214440_at [Chip: HT_HG-U133A];214440_at [Chip: U133A];214440_PM_at [Chip: U133_Plus_PM];214440_at [Chip: Focus];11748981_a_at [Chip: HG-U219]\t-\t-\t.....\t-\t-\t-\n'

dbFind: 'Input Value\tInput Type\tGene ID\nENSG00000121410\tEnsembl Gene ID\t1\nENSG00000171428\tEnsembl Gene ID\t9\n'

dbWalk: 'Ensembl Gene ID\tGene ID\tHomolog - Mouse Gene ID\tEnsembl Gene ID\nENSG00000121410\t1\t117586\tENSMUSG00000022347\nENSG00000171428\t9\t17961\tENSMUSG00000051147\n'

dbOrtho: 'Gene Symbol\tGene ID\nMYC\t17869;107771\nCPT1A\t12894\n'