udel-cbcb/iPTMnetR
Interface to the 'iPTMnet' API

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docs/api.md

docs/api.md
In udel-cbcb/iPTMnetR: Interface to the 'iPTMnet' API

API

The API consists of functions that mirror the functionality of the iPTMNet rest api.

search

Search the iptmnet database for the given search term.

Usage

search_iptmnet(search_term = "term",term_type=TermType()$TYPE,Role()$ROLE,ptm_vector=c(),organism_vector=c())

Arguments

| Name | Description | |-|-| | search_term| The term that you want to search in the database | |term_type| The type of the term that is being searched. It can be All,UniprotID,Protein/Gene Name,PMID | |role| The role to be filtered upon. It can be Enzyme or Substrate,Enzyme,Substrate,Enzyme and Substrate | |ptm_vector| A vector containing ptm types to filter upon. It can contain following values Acetylation,C-Glycosylation,Myristoylation,Ubiquitination,N-Glycosylation,S-Glycosylation,Phosphorylation,S-Nitrosylation,O-Glycosylation,Methylation,Sumoylation. Passing an empty vector will match against all possible values. | |organism_vector| A vector containing taxon codes for orgaism to filter upon. |

Example

search("Smad2",TermType()$ProteinOrGeneName,Role()$EnzymeOrSubstrate)

Output

iptm_id | protein_name | gene_name | synonyms | organism_taxon_code | organism_species | organism_common_name | substrate_role | substrate_num | enzyme_role | enzyme_num | ptm_dependent_ppi_role | ptm_dep_ppi_num | sites | isoforms --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- O70436 | Mothers against decapentaplegic homolog 2; | Smad2 | Madh2 | 10116 | Rattus norvegicus | Rat | True | 0 | False | 0 | False | 0 | 6 | 0 Q1W668 | Mothers against decapentaplegic homolog 2; | SMAD2 | | 9913 | Bos taurus | Bovine | True | 0 | False | 0 | False | 0 | 4 | 0

get_info

Get information for the given iptmnet_id

Usage

get_info(id = "iptmnet_id")

Arguments

| Name | Description | |-|-| | id| iPTMnet ID |

Example

get_info("Q15697")

Output

{
  "uniprot_ac": "Q15796",
  "uniprot_id": "SMAD2_HUMAN",
  "protein_name": "Mothers against decapentaplegic homolog 2;",
  "gene_name": "SMAD2",
  "synonyms": [
    "MADH2",
    "MADR2"
  ],
  "organism": {
    "taxon_code": 9606,
    "species": "Homo sapiens",
    "common_name": "Human"
  },
  "pro": {
    "id": "PR:Q15796",
    "name": "mothers against decapentaplegic homolog 2 (human)",
    "definition": "A smad2 that is encoded in the genome of human.",
    "short_label": "hSMAD2",
    "category": "organism-gene"
  }
}

get_msa

Not implemented yet

get_proteoforms

Get proteoforms for the given iptmnet_id

Usage

get_proteoforms(id="iptmnet_id")

Arguments

| Name | Description | |-|-| | id| iPTMnet ID |

Example

get_proteoforms("Q15796")

Output

pro_id | label | sites | ptm_enzyme_id | ptm_enzyme_label | source | --- | --- | --- | --- | --- | --- | PR:000025934 | hSMAD2/iso:1/Phos:1 | pS465,pS467 | PR:000025963 | transforming growth factor beta type II receptor homodimeric complex phosphorylated form (human) | PRO | PR:000025935 | hSMAD2/iso:1/Phos:2 | pS465,pS467 | PR:000025963 | transforming growth factor beta type II receptor homodimeric complex phosphorylated form (human) | PRO | PR:000025935 | hSMAD2/iso:1/Phos:2 | pT8,pT220,pS245,pS250,pS255 | PR:000026189 | hMAPK3/iso:1/Phos:1 | PRO |

get_ptm_dependent_ppi

Get Post translational modification(PTM) dependent Protein-Protein interactions for the given iptmnet_id

Usage

get_ptm_dependent_ppi(id="iptmnet_id")

Arguments

| Name | Description | |-|-| | id| iPTMnet ID |

Example

get_ptm_dependent_ppi("Q15796")

Output

ptm_type | substrate_uniprot_id | substrate_name | site | interactant_uniprot_id | interactant_name | association_type | source | pmid --- | --- | --- | --- | --- | --- | --- | --- | --- | Phosphorylation | P49841 | GSK3B | S9 | Q15796 | SMAD2 | increased_association | eFIP | 21996745 | Phosphorylation | Q15796 | SMAD2 | S467 | Q13485 | SMAD4 | association | eFIP | 9346908 |

get_ppi_for_proteoforms

Get Protein-Protein interactions along with corresponding proteoforms for the given iPTMnet ID

Usage

get_ppi_for_proteoforms(id="iptmnet_id")

Arguments

| Name | Description | |-|-| | id| iPTMnet ID |

Example

get_ppi_for_proteoforms("Q15796")

Output

protein_1_pro_id | protein_1_label | relation | protein_2_pro_id | protein_2_label | source | pmids --- | --- | --- | --- | --- | --- | --- | --- | PR:000025934 | hSMAD2/iso:1/Phos:1 | Interaction | PR:Q13485 | hSMAD4 | PRO | 9311995 PR:000025935 | hSMAD2/iso:1/Phos:2 | Interaction | PR:Q13485 | hSMAD4 | PRO | 12193595 PR:000045371 | hSMAD2/iso:1/UnPhos:1 | Interaction | | | PRO | 8980228

get_ptm_enzymes_from_list

Get PTM enzymes for a list of sites.

Usage

get_ptm_enzymes_from_list(sites=list())

Arguments

| Name | Description | |-|-| | sites| list of sites. Each site should have the following attributes: substrate_ac, site_residue, site_position |

Example

# create a list of sites
sites = list(
    list(
      substrate_ac="Q15796",
      site_residue="K",
      site_position="19"
    ),
    list(
      substrate_ac="Q15796",
      site_residue="T",
      site_position="8"
    ),
    list(
      substrate_ac="P04637",
      site_residue="K",
      site_position="120"
    )
  )

# perform the query
get_ptm_enzymes_from_list(sites)

Output

ptm_type | site | site_position | score | source | pmid | enz_name | enz_id | sub_name | sub_id | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | Acetylation | K120 | 120 | 2 | UniProt | 23431171 | KAT6A | Q92794 | TP53 | P04637 | Phosphorylation | T8 | 8 | 3 | nextProt | 19201832,15241418 | CDK2 | P24941 | SMAD2 | Q15796 |

get_ptm_enzymes_from_file

Get PTM enzymes for sites in the given csv file

Usage

get_ptm_enzymes_from_file(file_name='/path/to/file.csv')

Arguments

| Name | Description | |-|-| | file_name| Path to the csv file containing the list of sites . First line should be a header with following attributes: substrate_ac, site_residue, site_position |

Example


# perform the query
get_ptm_enzymes_from_file("sites.csv")

Output

ptm_type | site | site_position | score | source | pmid | enz_name | enz_id | sub_name | sub_id | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | Acetylation | K120 | 120 | 2 | UniProt | 23431171 | KAT6A | Q92794 | TP53 | P04637 | Phosphorylation | T8 | 8 | 3 | nextProt | 19201832,15241418 | CDK2 | P24941 | SMAD2 | Q15796 |

get_ptm_ppi_from_list

Get Post translational modification(PTM) dependent Protein-Protein interactions(PPI) for the given list of site

Usage

get_ptm_ppi_from_list(sites=list())

Arguments

| Name | Description | |-|-| | sites| list of sites. Each site should have the following attributes: substrate_ac, site_residue, site_position |

Example

# create a list of sites
sites = list(
    list(
      substrate_ac="Q15796",
      site_residue="K",
      site_position="19"
    ),
    list(
      substrate_ac="Q15796",
      site_residue="T",
      site_position="8"
    ),
    list(
      substrate_ac="P04637",
      site_residue="K",
      site_position="120"
    )
  )

# perform the query
get_ptm_ppi_from_list(sites)

Output

ptm_type | site | site_position | association_type | source | pmids | interactant_id | interactant_name | --- | --- | --- | --- | --- | --- | --- | --- | Phosphorylation | S378 | 378 | association | rlimsp | 27462439 | Q92540 | SMG7 | Phosphorylation | S378 | 378 | increased_association | rlimsp | 22911849 | P08047 | SP1 |

get_ptm_ppi_from_file

Get Post translational modification(PTM) dependent Protein-Protein interactions(PPI) for sites in the given csv

Usage

get_ptm_ppi_from_file(file_name="/path/to/file.csv")

Arguments

| Name | Description | |-|-| | file_name| Path to the csv file containing the list of sites . First line should be a header with following attributes: substrate_ac, site_residue, site_position |

Example

# perform the query
get_ptm_ppi_from_file("sites.csv")

Output

ptm_type | site | site_position | association_type | source | pmids | interactant_id | interactant_name | --- | --- | --- | --- | --- | --- | --- | --- | Phosphorylation | S378 | 378 | association | rlimsp | 27462439 | Q92540 | SMG7 | Phosphorylation | S378 | 378 | increased_association | rlimsp | 22911849 | P08047 | SP1 |

set_host_url

Set the URL of the iPTMnet API server. By default the client points to the public iPTMnet api server located at - https://annotation.dbi.udel.edu/iptmnet/api

Usage

set_host_url(url="http://localhost.com")

Arguments

| Name | Description | |-|-| | url| URL of the iPTMnet api server|

set_api_version

Set the Version of the iPTMnet API to use. By default the client uses - v1

Usage

set_api_version(version="v1")

Arguments

| Name | Description | |-|-| | version| Version of the API to use|



udel-cbcb/iPTMnetR documentation built on Nov. 14, 2021, 9:16 p.m.

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