data_formats.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

#
#  This file is part of the `pypath` python module
#
#  Copyright 2014-2023
#  EMBL, EMBL-EBI, Uniklinik RWTH Aachen, Heidelberg University
#
#  Authors: see the file `README.rst`
#  Contact: Dénes Türei (turei.denes@gmail.com)
#
#  Distributed under the GPLv3 License.
#  See accompanying file LICENSE.txt or copy at
#      https://www.gnu.org/licenses/gpl-3.0.html
#
#  Website: https://pypath.omnipathdb.org/
#

from future.utils import iteritems

import os
import copy

# from pypath:
import pypath.internals.input_formats as input_formats
import pypath.resources.urls as urls
import pypath.share.common as common
import pypath_common._constants as _const


__all__ = [
    'reaction', 'interaction', 'interaction_misc', 'pathway',
    'interaction_htp', 'ptm', 'ptm_misc', 'obsolate',
    'transcription_deprecated', 'transcription_onebyone',
    'omnipath', 'transcription', 'negative',
    'gdsc_comp_target', 'cgc', 'reactome_modifications', 'reaction_misc',
    'ligand_receptor'
]

"""
Reaction databases.
These are not included in OmniPath, because only a minor
part of their content can be used when processing along
strict conditions to have only binary interactions with
references.
"""

reaction = {
    'Reaction resources': input_formats.NetworkInput(
        name = 'reaction resources',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (3, '1'),
        sign = None,
        resource = 4,
        input = 'reaction.get_reactions',
        references = (5, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'sif_rule': (2, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        data_model = 'process_description',
    ),
}

pathwaycommons_all = input_formats.NetworkInput(
    name = 'PathwayCommons',
    separator = None,
    id_col_a = 0,
    id_col_b = 2,
    id_type_a = 'genesymbol',
    id_type_b = 'genesymbol',
    entity_type_a = 'protein',
    entity_type_b = 'protein',
    is_directed = (
        1,
        [
            'state-change',
            'controls-phosphorylation-of',
            'controls-state-change-of',
            'controls-transport-of',
        ],
    ),
    sign = None,
    input = 'pathwaycommons.pathwaycommons_interactions',
    references = None,
    ncbi_tax_id = 9606,
    resource = 3,
    extra_edge_attrs = {
        'rule': 1,
    },
    extra_node_attrs_a = {},
    extra_node_attrs_b = {},
    must_have_references = False,
    input_args = {
        'types': {
            'state-change',
            'in-same-component',
            'interacts-with',
            'controls-state-change-of',
            'in-complex-with',
            'controls-transport-of',
            'controls-phosphorylation-of',
        },
    },
    data_model = 'activity_flow',
)


pathwaycommons_transcription_all = input_formats.NetworkInput(
    name = 'PathwayCommons',
    separator = None,
    id_col_a = 0,
    id_col_b = 2,
    id_type_a = 'genesymbol',
    id_type_b = 'genesymbol',
    entity_type_a = 'protein',
    entity_type_b = 'protein',
    is_directed = (
        1,
        'controls-expression-of',
    ),
    sign = None,
    input = 'pathwaycommons.pathwaycommons_interactions',
    references = None,
    ncbi_tax_id = 9606,
    interaction_type = 'transcriptional',
    resource = 3,
    extra_edge_attrs = {
        'rule': 1,
    },
    extra_node_attrs_a = {},
    extra_node_attrs_b = {},
    must_have_references = False,
    input_args = {
        'types': {
            'controls-expression-of',
        },
    },
    data_model = 'activity_flow',
)


def _pathwaycommons_single_resource(resource, transcription = False):

    dmodel_interaction = {'CORUM', 'IntAct', 'DIP', 'BioGRID', 'BIND', 'INOH'}

    _pathwaycommons_all = (
        pathwaycommons_transcription_all
            if transcription else
        pathwaycommons_all
    )

    input_def = copy.deepcopy(_pathwaycommons_all)
    input_def.input_args['resources'] = resource
    input_def.data_model = (
        'interaction'
            if resource in dmodel_interaction else
        'activity_flow'
    )

    return input_def


_pathwaycommons_resources = (
    'NCI-PID',
    'KEGG',
    'CORUM',
    'BIND',
    'HPRD',
    'WikiPathways',
    'INOH',
    'BioGRID',
    'NetPath',
    'Reactome',
    'DIP',
    'IntAct',
    'PANTHER',
    'PhosphoSite',
)


pathwaycommons = dict(
    (
        resource.lower().replace('-', '_'),
        _pathwaycommons_single_resource(resource),

    )
    for resource in _pathwaycommons_resources
)

pathwaycommons_transcription = dict(
    (
        resource.lower().replace('-', '_'),
        _pathwaycommons_single_resource(resource, transcription = True),

    )
    for resource in _pathwaycommons_resources
)


# synonym for old name
reactome_pc = pathwaycommons['reactome']


reaction_misc = {
    'nci_pid': input_formats.NetworkInput(
        name = 'NCI-PID',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, 'directed'),
        sign = False,
        ncbi_tax_id = 9606,
        input = 'reaction.pid_interactions',
        references = (3, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'process_description',
    ),
    'acsn': input_formats.NetworkInput(
        name = 'ACSN',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, 'directed'),
        sign = False,
        ncbi_tax_id = 9606,
        input = 'acsn.acsn_interactions',
        references = (3, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'process_description',
    ),
    'reactome': input_formats.NetworkInput(
        name = 'Reactome',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, 'directed'),
        sign = False,
        ncbi_tax_id = 9606,
        huge = True,
        input = 'reaction.reactome_interactions',
        input_args = {'ask': False},
        references = (3, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'process_description',
    ),
}

reaction_pc = {
    'acsn': input_formats.NetworkInput(
        name = 'ACSN',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (
            2,
            [
                'UNKNOWN_TRANSITION',
                'INTERACTION_TYPE',
                'KNOWN_TRANSITION_OMITTED',
                'INHIBITION',
                'UNKNOWN_POSITIVE_INFLUENCE',
                'UNKNOWN_CATALYSIS',
                'POSITIVE_INFLUENCE',
                'STATE_TRANSITION',
                'TRANSLATION',
                'UNKNOWN_NEGATIVE_INFLUENCE',
                'NEGATIVE_INFLUENCE',
                'MODULATION',
                'TRANSCRIPTION',
                'COMPLEX_EXPANSION',
                'TRIGGER',
                'CATALYSIS',
                'PHYSICAL_STIMULATION',
                'UNKNOWN_INHIBITION',
                'TRANSPORT',
                'inhibits',
                'activates',
            ],
            ';',
        ),
        sign = (
            2,
            [
                'TRIGGER',
                'UNKNOWN_POSITIVE_INFLUENCE',
                'POSITIVE_INFLUENCE',
                'PHYSICAL_STIMULATION',
                'activates',
            ],
            [
                'INHIBITION',
                'UNKNOWN_NEGATIVE_INFLUENCE',
                'NEGATIVE_INFLUENCE',
                'inhibits',
            ],
            ';',
        ),
        ncbi_tax_id = 9606,
        negative_filters = [
            (
                2,
                [
                    'COMPLEX_EXPANSION',
                    'TRANSCRIPTION',
                ],
                ';'
            ),
        ],
        positive_filters = [],
        references = (3, ';'),
        input = 'acsn.acsn_interactions',
        header = False,
        extra_edge_attrs = {
            'effect': (2, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'process_description',
    ),
}


"""
Pathway databases included in OmniPath.
These are manually curated, directed, and in most
of the cases signed interactions, with literature references.
"""
pathway = {
    'trip': input_formats.NetworkInput(
        name = 'TRIP',
        separator = None,
        id_col_a = 1,
        id_col_b = 0,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, ['stimulation', 'inhibition']),
        sign = (4, 'stimulation', 'inhibition'),
        ncbi_tax_id = 9606,
        input = 'trip.trip_interactions',
        references = (2, ';'),
        header = False,
        extra_edge_attrs = {
            'method': (3, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'spike': input_formats.NetworkInput(
        name = 'SPIKE',
        separator = '\t',
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, ['1']),
        sign = (7, '1', '2'),
        input = 'spike.spike_interactions',
        references = (5, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'effect': 7,
            'mechanism': 11,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'signalink3': input_formats.NetworkInput(
        name = 'SignaLink3',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (3, True),
        sign = (4, 1, -1),
        input = 'signalink.signalink_interactions',
        references = 9,
        resource = 10,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        positive_filters = [(2, True)], # only direct interactions
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'guide2pharma': input_formats.NetworkInput(
        name = 'Guide2Pharma',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'genesymbol',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (7, 1, -1),
        input = 'guide2pharma.guide2pharma_interactions',
        references = 11,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {'g2p_ligand_location': 8},
        extra_node_attrs_b = {'g2p_target_type': 9},
        data_model = 'ligand_receptor',
    ),
    'ca1': input_formats.NetworkInput(
        name = 'CA1',
        id_col_a = 1,
        id_col_b = 6,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (10, ['_', '+']),
        sign = (10, '+', '_'),
        header = False,
        input = 'ca1.ca1_interactions',
        references = (12, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'effect': 10,
            'type': 11,
        },
        extra_node_attrs_a = {
            'ca1_location': 4,
            'ca1_function': 3,
        },
        extra_node_attrs_b = {
            'ca1_location': 9,
            'ca1_function': 8,
        },
        data_model = 'activity_flow',
    ),
    'arn': input_formats.NetworkInput(
        name = 'ARN',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (3, ['1', '2']),
        sign = (4, '1', '-1'),
        input = 'netbiol.arn_interactions',
        references = (7, ':'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'effect': 4,
            'is_direct': 2,
            'is_directed': 3
        },
        extra_node_attrs_a = {'atg': 5},
        extra_node_attrs_b = {'atg': 6},
        data_model = 'activity_flow',
    ),
    'nrf2': input_formats.NetworkInput(
        name = 'NRF2ome',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (3, ['1', '2']),
        sign = (4, '1', '-1'),
        input = 'netbiol.nrf2ome_interactions',
        references = (5, ':'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'effect': 4,
            'is_direct': 2,
            'is_directed': 3
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'macrophage': input_formats.NetworkInput(
        name = 'Macrophage',
        separator = ';',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (3, ['1']),
        sign = (2, 'Activation', 'Inhibition'),
        input = 'macrophage.macrophage_interactions',
        references = (5, ','),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'type': (2, ','),
            'location': (4, ',')
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'death': input_formats.NetworkInput(
        name = 'DeathDomain',
        separator = '\t',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'deathdomain.deathdomain_interactions_rescued',
        references = (3, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (2, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'pdz': input_formats.NetworkInput(
        name = 'PDZBase',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = {
            'col': 7,
            'include': {9606},
        },
        input = 'pdzbase.pdzbase_interactions',
        references = 8,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'signor': input_formats.NetworkInput(
        name = 'SIGNOR',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        # only direct interactions
        positive_filters = [(10, True)],
        # exclude TF-target interactions
        negative_filters = [
            (
                7,
                {
                    'transcriptional regulation',
                    'transcriptional activation',
                    'transcriptional repression',
                }
            ),
        ],
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (
            6,
            {
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity',
                'up-regulates quantity by stabilization',
                'up-regulates quantity by expression',
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
                'down-regulates quantity',
                'down-regulates quantity by repression',
            }
        ),
        sign = (
            6,
            {
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity',
                'up-regulates quantity by stabilization',
                'up-regulates quantity by expression',
            },
            {
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
                'down-regulates quantity',
                'down-regulates quantity by repression',
            }
        ),
        input = 'signor.signor_interactions',
        references = (9, ';'),
        header = False,
        extra_edge_attrs = {
            'mechanism': (7, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'adhesome': input_formats.NetworkInput(
        name = 'Adhesome',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (2, ('+', '_')),
        sign = (2, '+', '_'),
        input = 'adhesome.adhesome_interactions',
        references = 4,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'icellnet': input_formats.NetworkInput(
        name = 'ICELLNET',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        sign = None,
        input = 'icellnet.icellnet_interactions',
        references = 6,
        resource = 5,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'celltalkdb': input_formats.NetworkInput(
        name = 'CellTalkDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        sign = None,
        input = 'celltalkdb.celltalkdb_interactions',
        references = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'cellchatdb': input_formats.NetworkInput(
        name = 'CellChatDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        sign = (4, 'stimulation', 'inhibition'),
        input = 'cellchatdb.cellchatdb_interactions',
        input_args = {'cofactors': False},
        references = 6,
        header = False,
        extra_edge_attrs = {
            'category': 7,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'connectomedb': input_formats.NetworkInput(
        name = 'connectomeDB2020',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        input = 'connectomedb.connectomedb_interactions',
        references = 3,
        header = False,
        data_model = 'ligand_receptor',
    ),
    'talklr': input_formats.NetworkInput(
        name = 'talklr',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        input = 'talklr.talklr_interactions',
        references = 2,
        resource = 3,
        header = False,
        extra_edge_attrs = {
            'putative': 4,
        },
        data_model = 'ligand_receptor',
    ),
    'cellinker': input_formats.NetworkInput(
        name = 'Cellinker',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        input = 'cellinker.cellinker_lr_interactions',
        references = (5, ';'),
        resource = (4, ';'),
        header = False,
        extra_edge_attrs = {
            'type': 6,
        },
        data_model = 'ligand_receptor',
    ),
    'scconnect': input_formats.NetworkInput(
        name = 'scConnect',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        positive_filters = [
            (4, {'protein', 'complex'}),
            (5, {'protein', 'complex'}),
        ],
        ncbi_tax_id = {
            'A': {'col': 2},
            'B': {'col': 3},
        },
        only_default_organism = True,
        is_directed = True,
        sign = (
            6,
            [
                'Activation',
                'Activator',
                'Agonist',
                'Biased agonist',
                'Full agonist',
                'Irreversible agonist',
                'Partial agonist',
                'Positive',
                'Potentiation',
                'Slows inactivation',
            ],
            [
                'Antagonist',
                'Antibody',
                'Channel blocker',
                'Competitive',
                'Feedback inhibition',
                'Inhibition',
                'Inhibitor',
                'Irreversible agonist'
                'Irreversible inhibition',
                'Negative',
                'Pore blocker',
                'Voltage-dependent inhibition',
            ],
        ),
        input = 'scconnect.scconnect_interactions',
        references = (7, '|'),
        header = False,
        data_model = 'ligand_receptor',
    ),
}

# synonym
activity_flow = pathway

"""
Pathway (activity flow) resources without literature references.
"""
pathway_noref = {
    'kegg': input_formats.NetworkInput(
        name = 'KEGG',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (2, ('activation', 'inhibition')),
        sign = (2, 'activation', 'inhibition'),
        input = 'kegg.kegg_interactions',
        references = False,
        must_have_references = False,
        header = False,
        positive_filters = [
            (5, True), # is_direct
        ],
        negative_filters = [
            (6, True), # transcriptional
        ],
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'wang': input_formats.NetworkInput(
        name = 'Wang',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'entrez',
        id_type_b = 'entrez',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (4, ('+', '-')),
        sign = (4, '+', '-'),
        input = 'wang.wang_interactions',
        references = False,
        must_have_references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'cui': input_formats.NetworkInput(
        name = 'Cui2007',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'entrez',
        id_type_b = 'entrez',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (4, ('+', '-')),
        sign = (4, '+', '-'),
        input = 'wang.cui_interactions',
        references = False,
        must_have_references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'kegg-medicus': input_formats.NetworkInput(
        name = 'KEGG-MEDICUS',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (5, ('stimulation', 'inhibition')),
        sign = (5, 'stimulation', 'inhibition'),
        input = 'kegg.kegg_medicus_interactions',
        references = False,
        must_have_references = False,
        header = False,
        positive_filters = [
            (4, 'post_translational'),
        ],
        negative_filters = [
            (5, ['missing', 'enzyme_enzyme']),
        ],
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'spike_lc': input_formats.NetworkInput(
        name = 'SPIKE_LC',
        separator = '\t',
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, ['1']),
        sign = (7, '1', '2'),
        input = 'spike.spike_interactions',
        references = (5, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'effect': 7,
            'mechanism': 11,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        input_args = {'min_confidence': 99},
        data_model = 'activity_flow',
    ),
}


# synonym
pathwayextra = pathway_noref

pathway_all = dict(copy.deepcopy(pathway), **copy.deepcopy(pathway_noref))


pathway_bad = {
    'laudanna_effects': input_formats.NetworkInput(
        name = 'Laudanna-effects',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (2, ('activation', 'inhibition')),
        sign = (2, 'activation', 'inhibition'),
        input = 'laudanna.laudanna_effects',
        references = False,
        must_have_references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'laudanna_directions': input_formats.NetworkInput(
        name = 'Laudanna-directions',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        input = 'laudanna.laudanna_directions',
        references = False,
        must_have_references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
}

"""
Interaction databases included in OmniPath.
These are subsets of the named databases, having
only low throughput, manually curated, undirected
interactions with literature references.
"""
interaction = {
    'biogrid': input_formats.NetworkInput(
        name = 'BioGRID',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'biogrid.biogrid_interactions',
        references = (2, '|'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'ccmap': input_formats.NetworkInput(
        name = 'CancerCellMap',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (2, 'directed'),
        sign = False,
        ncbi_tax_id = 9606,
        input = 'cancercellmap.ccmap_interactions',
        references = (3, ';'),
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'mppi': input_formats.NetworkInput(
        name = 'MPPI',
        separator = '|',
        id_col_a = 2,
        id_col_b = 6,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'mppi.mppi_interactions',
        references = (0, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'evidence': (1, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'dip': input_formats.NetworkInput(
        name = 'DIP',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'dip.dip_interactions',
        references = (2, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (4, ';'),
            'type': (3, ';'),
            'id': 5,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'netpath': input_formats.NetworkInput(
        name = 'NetPath',
        separator = None,
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'entrez',
        id_type_b = 'entrez',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'netpath.netpath_interactions',
        references = (4, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (5, ';'),
            'type': (6, ';'),
            'pathway': (7, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'innatedb': input_formats.NetworkInput(
        name = 'InnateDB',
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'innatedb.innatedb_interactions',
        references = (4, ':'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'intact': input_formats.NetworkInput(
        name = 'IntAct',
        separator = ',',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'intact.intact_interactions',
        references = 4,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': 5,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'lit17': input_formats.NetworkInput(
        name = 'Lit-BM-17',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        references = (2, ';'),
        input = 'huri.lit_bm_17_interactions',
        header = False,
        extra_edge_attrs = {
            'mentha_score': 3,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'alz': input_formats.NetworkInput(
        name = 'AlzPathway',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = urls.urls['alzpathway']['url'],
        references = (8, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'matrixdb': input_formats.NetworkInput(
        name = 'MatrixDB',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'matrixdb.matrixdb_interactions',
        references = (2, '|'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (3, '|'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
}
"""
PTM databases included in OmniPath.
These supply large sets of directed interactions.
"""
ptm = {
    'psite': input_formats.NetworkInput(
        name = 'PhosphoSite',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        input = 'phosphosite.phosphosite_interactions_curated',
        references = (5, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'evidence': (4, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'depod': input_formats.NetworkInput(
        name = 'DEPOD',
        separator = ';',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        input = 'depod.depod_interactions',
        references = (2, '|'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'lmpid': input_formats.NetworkInput(
        name = 'LMPID',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 0,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'lmpid.lmpid_interactions',
        references = (2, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'phelm': input_formats.NetworkInput(
        name = 'phosphoELM',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = {
            'col': 3,
            'dict': {
                'Homo sapiens': 9606,
            },
        },
        input = 'phosphoelm.phosphoelm_interactions',
        references = (2, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'elm': input_formats.NetworkInput(
        name = 'ELM',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 0,
        sign = False,
        ncbi_tax_id = {
            'A': {'col': 13, 'include': {9606}},
            'B': {'col': 14, 'include': {9606}},
        },
        input = 'elm.elm_interactions',
        references = 12,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'domino': input_formats.NetworkInput(
        name = 'DOMINO',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 0,
        sign = False,
        ncbi_tax_id = {
            'A': {
                'col': 6,
                'dict': {
                    '9606': 9606
                }
            },
            'B': {
                'col': 7,
                'dict': {
                    '9606': 9606
                }
            }
        },
        input = 'domino.domino_interactions',
        references = (5, ';'),
        header = False,
        extra_edge_attrs = {
            'method': (4, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'dbptm': input_formats.NetworkInput(
        name = 'dbPTM',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = ['genesymbol', 'uniprot'],
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'dbptm.dbptm_interactions',
        references = (2, ';'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = True,
        data_model = 'enzyme_substrate',
    ),
    'hprd_p': input_formats.NetworkInput(
        name = 'HPRD-phos',
        separator = None,
        id_col_a = 6,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'refseqp',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'hprd.hprd_interactions',
        references = (10, ','),
        header = False,
        extra_edge_attrs = {
            'mechanism': 8,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'kea': input_formats.NetworkInput(
        name = 'KEA',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'kea.kea_interactions',
        references = 4,
        resource = 5,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = True,
        data_model = 'enzyme_substrate',
    ),
    'iptmnet': input_formats.NetworkInput(
        name = 'iPTMnet',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'iptmnet.iptmnet_interactions',
        references = 8,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = True,
        data_model = 'enzyme_substrate',
    ),
}

# synonym
enzyme_substrate = ptm

"""
Other PTM datasets which are not used because the lack of
references.
"""
ptm_misc = {
    'psite_noref': input_formats.NetworkInput(
        name = 'PhosphoSite_noref',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'phosphosite.phosphosite_interactions_noref',
        references = False,
        extra_edge_attrs = {
            'evidence': (4, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'ppoint': input_formats.NetworkInput(
        name = 'PhosphoPoint',
        separator = ';',
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        header = True,
        ncbi_tax_id = 9606,
        input = 'phosphopoint.phosphopoint_interactions',
        references = False,
        sign = False,
        extra_edge_attrs = {
            'category': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'pnetworks': input_formats.NetworkInput(
        name = 'PhosphoNetworks',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'phosphonetworks.phosphonetworks_interactions',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'mimp': input_formats.NetworkInput(
        name = 'MIMP',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'mimp.mimp_interactions',
        references = False,
        resource = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'li2012': input_formats.NetworkInput(
        name = 'Li2012',
        separator = False,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        input = 'li2012.li2012_interactions',
        references = False,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'mechanism': 3,
            'route': 2,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'enzyme_substrate',
    ),
    'protmapper': input_formats.NetworkInput(
        name = 'ProtMapper',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 1,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'protmapper.protmapper_interactions',
        references = 3,
        resource = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        data_model = 'enzyme_substrate',
    ),
}

# synonym
ptm_noref = ptm_misc
kinaseextra = ptm_misc

ptm_all = copy.deepcopy(ptm_misc)
ptm_all.update(ptm)

extra_directions = copy.deepcopy(ptm_misc)
extra_directions.update(copy.deepcopy(pathway_noref))
extra_directions['acsn'] = copy.deepcopy(reaction_pc['acsn'])

"""
Interaction databases not included in OmniPath.
These were omitted because lack of references,
or because we could not separate the low throughput,
manually curated interactions.
"""
interaction_misc = {
    'hippie': input_formats.NetworkInput(
        name = 'HIPPIE',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'hippie.hippie_interactions',
        references = 4,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'biogrid': input_formats.NetworkInput(
        name = 'BioGRID',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'biogrid.biogrid_interactions',
        references = (2, '|'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'hi2': input_formats.NetworkInput(
        name = 'HI-II',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.rolland_hi_ii_14',
        references = False,
        header = False,
        extra_edge_attrs = {
            'numof_screens': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'lit13': input_formats.NetworkInput(
        name = 'Lit-BM-13',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.lit_bm_13_interactions',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'huri': input_formats.NetworkInput(
        name = 'HuRI',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.huri_interactions',
        references = False,
        header = True,
        extra_edge_attrs = {
            'score': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'hi_union': input_formats.NetworkInput(
        name = 'HI-union',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.hi_union_interactions',
        references = False,
        header = True,
        extra_edge_attrs = {
            'score': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'yu2011': input_formats.NetworkInput(
        name = 'Yu2011',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.yu2011_interactions',
        references = False,
        header = True,
        extra_edge_attrs = {
            'score': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'yang2016': input_formats.NetworkInput(
        name = 'Yang2016',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.yang2016_interactions',
        references = False,
        header = True,
        extra_edge_attrs = {
            'score': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'cpdb': input_formats.NetworkInput(
        name = 'CPDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot-entry',
        id_type_b = 'uniprot-entry',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'cpdb.cpdb_interactions',
        references = (3, ','),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
}

interaction_misc['acsn'] = copy.deepcopy(reaction_pc['acsn'])


interaction_deprecated = {
    'hi3_local': input_formats.NetworkInput(
        name = 'HI-III',
        separator = None,
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        # note: obtain the file yourself, and replace
        # this location
        input = '/home/denes/Documents/pw/data/hi3-2.3.tsv',
        references = False,
        header = True,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'hi3_local_2': input_formats.NetworkInput(
        name = 'Vidal HI-III',
        separator = None,
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.vidal_hi_iii',
        references = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        # note: obtain the file yourself, and replace
        # this location
        input_args = {'fname': '/home/denes/Documents/pw/data/hi3-2.3.tsv'},
        data_model = 'interaction',
    ),
    'hi3': input_formats.NetworkInput(
        name = 'HI-III',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'huri.hi_iii',
        references = False,
        header = True,
        extra_edge_attrs = {
            'score': 5,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'hsn': input_formats.NetworkInput(
        name = 'HumanSignalingNetwork',
        separator = None,
        id_col_a = 2,
        id_col_b = 3,
        id_type_a = 'entrez',
        id_type_b = 'entrez',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, ['+', '-']),
        sign = (4, '+', '-'),
        input = 'wang.hsn_interactions',
        references = False,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
}


interaction_htp = {
    'hprd': input_formats.NetworkInput(
        name = 'HPRD',
        separator = None,
        id_col_a = 0,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 0,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'hprd.hprd_interactions_htp',
        references = (7, ','),
        header = False,
        extra_edge_attrs = {
            'method': (6, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'intact': input_formats.NetworkInput(
        name = 'IntAct',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'intact.intact_interactions',
        references = 4,
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        input_args = {'miscore': 0.0},
        data_model = 'interaction',
    ),
    'biogrid': input_formats.NetworkInput(
        name = 'BioGRID',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'biogrid.biogrid_interactions',
        references = (2, '|'),
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        input_args = {
            'htp_limit': None,
            'ltp': False,
        },
        data_model = 'interaction',
    ),
    'dip': input_formats.NetworkInput(
        name = 'DIP',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'dip.dip_interactions',
        references = (2, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (4, ';'),
            'type': (3, ';'),
            'id': 5,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        input_args = {
            'core_only': False,
            'small_scale_only': False,
        },
        data_model = 'interaction',
    ),
    'ccmap': input_formats.NetworkInput(
        name = 'CancerCellMap',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 2,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'cancercellmap.ccmap_interactions',
        references = (3, ';'),
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'innatedb': input_formats.NetworkInput(
        name = 'InnateDB',
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'innatedb.innatedb_interactions',
        references = (4, ':'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'matrixdb': input_formats.NetworkInput(
        name = 'MatrixDB',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'matrixdb.matrixdb_interactions',
        references = (2, '|'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'method': (3, '|'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
    'mppi': input_formats.NetworkInput(
        name = 'MPPI',
        separator = '|',
        id_col_a = 2,
        id_col_b = 6,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'mppi.mppi_interactions',
        references = (0, ';'),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'evidences': (1, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'interaction',
    ),
}

"""
Transcriptional regulatory interactions.
"""
transcription_onebyone = {
    'abs': input_formats.NetworkInput(
        name = 'ABS',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'embl_id',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'abs.abs_interactions',
        interaction_type = 'transcriptional',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'encode_dist': input_formats.NetworkInput(
        name = 'ENCODE-distal',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'http://encodenets.gersteinlab.org/enets3.Distal.txt',
        interaction_type = 'transcriptional',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'encode_prox': input_formats.NetworkInput(
        name = 'ENCODE-proximal',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'http://encodenets.gersteinlab.org/enets2.Proximal_filtered.txt',
        interaction_type = 'transcriptional',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'pazar': input_formats.NetworkInput(
        name = 'PAZAR',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'enst',
        id_type_b = 'ensembl',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'pazar.pazar_interactions',
        interaction_type = 'transcriptional',
        references = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'htri': input_formats.NetworkInput(
        name = 'HTRIdb',
        separator = None,
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'htri.htri_interactions',
        interaction_type = 'transcriptional',
        references = 4,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'oreganno': input_formats.NetworkInput(
        name = 'ORegAnno',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'oreganno.oreganno_interactions',
        interaction_type = 'transcriptional',
        references = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'signor': input_formats.NetworkInput(
        name = 'SIGNOR',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        # only direct TF-target interactions
        positive_filters = [
            (10, True),
            (
                7,
                {
                    'transcriptional regulation',
                    'transcriptional activation',
                    'transcriptional repression',
                }
            ),
        ],
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (
            6,
            {
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity',
                'up-regulates quantity by stabilization',
                'up-regulates quantity by expression',
            },
            {
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
                'down-regulates quantity',
                'down-regulates quantity by repression',
            }
        ),
        input = 'signor.signor_interactions',
        references = (9, ';'),
        header = True,
        extra_edge_attrs = {
            'mechanism': (7, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        interaction_type = 'transcriptional',
        data_model = 'activity_flow',
    ),
    'kegg': input_formats.NetworkInput(
        name = 'KEGG',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (2, ('repression', 'expression')),
        sign = (2, 'expression', 'repression'),
        input = 'kegg.kegg_interactions',
        references = False,
        must_have_references = False,
        header = False,
        positive_filters = [
            (5, True), # is_direct
            (6, True), # transcriptional
        ],
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        interaction_type = 'transcriptional',
        data_model = 'activity_flow',
    ),
    'kegg-medicus': input_formats.NetworkInput(
        name = 'KEGG-MEDICUS',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = (5, ('stimulation', 'inhibition')),
        sign = (5, 'stimulation', 'inhibition'),
        input = 'kegg.kegg_medicus_interactions',
        references = False,
        must_have_references = False,
        header = False,
        positive_filters = [
            (4, 'transcriptional'),
        ],
        negative_filters = [
            (5, ['missing', 'enzyme_enzyme']),
        ],
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        interaction_type = 'transcriptional',
        data_model = 'activity_flow',
    ),
    'trrust': input_formats.NetworkInput(
        name = 'TRRUST',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (2, 'Activation', 'Repression'),
        ncbi_tax_id = 9606,
        input = 'trrust.trrust_interactions',
        interaction_type = 'transcriptional',
        references = 3,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
}

"""
New default transcription dataset is only TFregulons
as it is already an integrated resource and
has sufficient coverage.

Example
-------
import pypath

# load only `A` confidence level:
pypath.data_formats.transcription['tfregulons'].input_args['levels'] = {'A'}
pa = pypath.PyPath()
pa.init_network(pypath.data_formats.transcription)

pypath.data_formats.transcription['tfregulons'].input_args['levels'] = {
    'A', 'B', 'C', 'D'
}
pa = pypath.PyPath()
pa.init_network(pypath.data_formats.transcription)

"""
transcription_dorothea_old = {
    'dorothea': input_formats.NetworkInput(
        name = 'DoRothEA',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (2, '1', '-1'),
        ncbi_tax_id = 9606,
        input = 'dorothea.dorothea_interactions_old',
        interaction_type = 'transcriptional',
        resource = (12, ','),
        references = (13, ','),
        header = False,
        extra_edge_attrs = {
            'curated': 4,
            'chipseq': 5,
            'tfbs':    6,
            'coexp':   7,
            'level':   3,
            'kegg_pathways': (14, '|'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        data_model = 'activity_flow',
    ),
}


transcription_dorothea = {
    'dorothea': input_formats.NetworkInput(
        name = 'DoRothEA',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (2, 1, -1),
        ncbi_tax_id = 9606,
        input = 'dorothea.dorothea_interactions',
        interaction_type = 'transcriptional',
        resource = (12, ','),
        references = (13, ','),
        header = False,
        extra_edge_attrs = {
            'curated': 4,
            'chipseq': 5,
            'tfbs':    6,
            'coexp':   7,
            'level':   3,
        },
        input_args = {
            'levels': {'A', 'B', 'C', 'D'},
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        must_have_references = False,
        data_model = 'activity_flow',
    ),
}

# synonyms
dorothea = transcription_dorothea
tfregulons = transcription_dorothea

transcription_collectri = {
    'collectri': input_formats.NetworkInput(
        name = 'CollecTRI',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (2, 1, -1),
        ncbi_tax_id = 9606,
        input = 'collectri.collectri_interactions',
        interaction_type = 'transcriptional',
        resource = (4, ';'),
        references = (5, ';'),
        header = False,
        extra_edge_attrs = {
            'tf_category': 3,
            'sign_decision': 6
        },
        extra_node_attrs_a = {
            'tf_category': 3
        },
        extra_node_attrs_b = {},
        must_have_references = False,
        allow_loops = True,
        data_model = 'activity_flow',
    ),
}

# synonyms
collectri = transcription_collectri

# all transcriptional regulation resources
transcription = {}
transcription.update(copy.deepcopy(transcription_onebyone))
transcription.update(copy.deepcopy(transcription_dorothea))
transcription.update(copy.deepcopy(transcription_collectri))

"""
Old transctiptional regulation input formats.
Should not be used.
"""
transcription_deprecated = {
    'oreganno_old': input_formats.NetworkInput(
        name = 'ORegAnno',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'get_oreganno_old',
        interaction_type = 'transcriptional',
        references = 2,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
    )
}

"""
miRNA-target resources
"""
mirna_target = {
    'mir2dis': input_formats.NetworkInput(
        name = 'miR2Disease',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'mir-mat-name',
        id_type_b = 'genesymbol',
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'mir2disease.mir2disease_interactions',
        interaction_type = 'post_transcriptional',
        references = None,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'mirdeath': input_formats.NetworkInput(
        name = 'miRDeathDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'mirbase',
        id_type_b = 'entrez',
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {
            'col': 2,
            'include': {9606},
        },
        input = 'mirdeathdb.mirdeathdb_interactions',
        interaction_type = 'post_transcriptional',
        references = 3,
        header = False,
        extra_edge_attrs = {
            'function': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'ncrdeath': input_formats.NetworkInput(
        name = 'ncRDeathDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'mirbase',
        id_type_b = 'genesymbol',
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {
            'col': 6,
            'include': {9606},
        },
        input = 'ncrdeathdb.ncrdeathdb_interactions',
        interaction_type = 'post_transcriptional',
        references = 5,
        header = False,
        positive_filters = [(2, 'miRNA')],
        negative_filters = [
            (5, 'prediction'),
            (1, {None}),
            (0, {None}),
        ],
        extra_edge_attrs = {
            'pathway': 3,
            'effect': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'mirecords': input_formats.NetworkInput(
        name = 'miRecords',
        separator = None,
        id_col_a = 0,
        id_col_b = 2,
        id_type_a = 'mir-mat-name',
        id_type_b = 'genesymbol',
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {
            'A': {'col': 3, 'include': {9606}},
            'B': {'col': 4, 'include': {9606}},
        },
        input = 'mirecords.mirecords_interactions',
        interaction_type = 'post_transcriptional',
        references = 5,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'mirtarbase': input_formats.NetworkInput(
        name = 'miRTarBase',
        separator = None,
        id_col_a = 1,
        id_col_b = 3,
        id_type_a = 'mir-mat-name',
        id_type_b = 'genesymbol',
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {
            'A': {'col': 2, 'include': {9606}},
            'B': {'col': 5, 'include': {9606}},
        },
        positive_filters = [(8, 'Functional MTI')],
        input = 'mirtarbase.mirtarbase_interactions',
        interaction_type = 'post_transcriptional',
        references = 9,
        header = False,
        extra_edge_attrs = {
            'method': (7, '//'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'signor': input_formats.NetworkInput(
        name = 'SIGNOR',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'mir-pre',
        id_type_b = 'uniprot',
        # only direct miRNA-target interactions
        positive_filters = [
            (10, True),
            (
                7,
                'post transcriptional regulation',
            ),
        ],
        entity_type_a = 'mirna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = (
            6,
            {
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity',
                'up-regulates quantity by stabilization',
                'up-regulates quantity by expression',
            },
            {
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
                'down-regulates quantity',
                'down-regulates quantity by repression',
            }
        ),
        input = 'signor.signor_interactions',
        references = (9, ';'),
        header = True,
        extra_edge_attrs = {
            'mechanism': (7, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        interaction_type = 'post_transcriptional',
        data_model = 'activity_flow',
    ),
}

# synonym
mirnatarget = mirna_target


tf_mirna = {
    'transmir': input_formats.NetworkInput(
        name = 'TransmiR',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'mir-mat-name',
        entity_type_a = 'protein',
        entity_type_b = 'mirna',
        is_directed = True,
        sign = (2, 'Activation', 'Repression'),
        ncbi_tax_id = 9606,
        input = 'transmir.transmir_interactions',
        interaction_type = 'mirna_transcriptional',
        references = 3,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'encode': input_formats.NetworkInput(
        name = 'ENCODE_tf-mirna',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'mir-mat-name',
        entity_type_a = 'protein',
        entity_type_b = 'mirna',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'encode.encode_tf_mirna_interactions',
        interaction_type = 'mirna_transcriptional',
        references = None,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
     'collectri': input_formats.NetworkInput(
        name = 'CollecTRI',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'mir-mat-name',
        entity_type_a = 'protein',
        entity_type_b = 'mirna',
        is_directed = True,
        sign = (2, 1, -1),
        ncbi_tax_id = 9606,
        input = 'collectri.collectri_interactions',
        interaction_type = 'transcriptional',
        resource = (4, ';'),
        references = (5, ';'),
        header = False,
        extra_edge_attrs = {
            'tf_category': 3,
            'sign_decision': 6
        },
        extra_node_attrs_a = {
            'tf_category': 3
        },
        extra_node_attrs_b = {},
        must_have_references = False,
        allow_loops = True,
        input_args = {
            'protein_coding': False,
            'mirna': True,
        },
        data_model = 'activity_flow',
    ),
}

lncrna_target = {
    'lncdisease': input_formats.NetworkInput(
        name = 'LncRNADisease',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'lncrna-genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'lncrna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {'col': 5, 'include': {9606}},
        positive_filters = [(2, 'RNA'), (3, 'Protein')],
        input = 'lncdisease.lncdisease_interactions',
        interaction_type = 'lncrna_post_transcriptional',
        references = 6,
        header = False,
        extra_edge_attrs = {
            'mechanism': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'lncrnadb': input_formats.NetworkInput(
        name = 'lncrnadb',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'lncrna-genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'lncrna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {'col': 3, 'include': {9606}},
        positive_filters = [(2, 'protein')],
        input = 'lncrnadb.lncrnadb_interactions',
        interaction_type = 'lncrna_post_transcriptional',
        references = 4,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
    'ncrdeath': input_formats.NetworkInput(
        name = 'ncRDeathDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'lncrna-genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'lncrna',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = {
            'col': 6,
            'include': {9606},
        },
        input = 'ncrdeathdb.ncrdeathdb_interactions',
        interaction_type = 'lncrna_post_transcriptional',
        references = 5,
        header = False,
        positive_filters = [(2, 'lncRNA')],
        negative_filters = [
            (5, 'prediction'),
            (1, {None}),
            (0, {None}),
        ],
        extra_edge_attrs = {
            'pathway': 3,
            'effect': 4,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
    ),
}

# synonym
lncrna_mrna = lncrna_target

ligand_receptor = {
    'ramilowski2015': input_formats.NetworkInput(
        name = 'Ramilowski2015',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = None,
        input = 'ramilowski2015.ramilowski_interactions',
        references = (2, ','),
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'source': (3, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        mark_source = 'ramilowski_ligand',
        mark_target = 'ramilowski_receptor',
        must_have_references = False,
        input_args = {
            'putative': False
        },
        data_model = 'ligand_receptor',
    ),
    'kirouac2010': input_formats.NetworkInput(
        name = 'Kirouac2010',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'kirouac2010.kirouac2010_interactions',
        references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        mark_source = 'kirouac_ligand',
        mark_target = 'kirouac_receptor',
        data_model = 'ligand_receptor',
    ),
    'hpmr': input_formats.NetworkInput(
        name = 'HPMR',
        separator = None,
        id_col_a = 2,
        id_col_b = 0,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (1, 'Ligand'),
        sign = False,
        ncbi_tax_id = 9606,
        input = 'hpmr.hpmr_interactions',
        references = (3, ';'),
        must_have_references = False,
        header = False,
        extra_edge_attrs = {
            'partner_role': 1,
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'cellphonedb': input_formats.NetworkInput(
        name = 'CellPhoneDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = (4, 'ligand-receptor'),
        sign = False,
        ncbi_tax_id = 9606,
        input = 'cellphonedb.cellphonedb_interactions',
        references = (3, ';'),
        resource = (2, ';'),
        must_have_references = False,
        header = False,
        extra_edge_attrs = {
            'type': 4,
            'is_ppi': 7,
        },
        extra_node_attrs_a = {
            'cellphonedb_type': 5,
        },
        extra_node_attrs_b = {
            'cellphonedb_type': 6,
        },
        positive_filters = [],
        data_model = 'ligand_receptor',
    ),
    'lrdb': input_formats.NetworkInput(
        name = 'LRdb',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'genesymbol',
        id_type_b = 'genesymbol',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'lrdb.lrdb_interactions',
        references = 3,
        resource = 2,
        must_have_references = False,
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'baccin2019': input_formats.NetworkInput(
        name = 'Baccin2019',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'baccin2019.baccin2019_interactions',
        references = 6,
        resource = 5,
        must_have_references = False,
        header = False,
        negative_filters = [
            (2, 'Incorrect'),
        ],
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {
            'baccin_category': 4,
            'baccin_location': 3,
        },
        data_model = 'ligand_receptor',
    ),
    'embrace': input_formats.NetworkInput(
        name = 'EMBRACE',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'embrace.embrace_interactions',
        must_have_references = False,
        header = False,
        data_model = 'ligand_receptor',
    ),
    'italk': input_formats.NetworkInput(
        name = 'iTALK',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = True,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'italk.italk_interactions',
        must_have_references = False,
        header = False,
        data_model = 'ligand_receptor',
    ),
    'wojtowicz2020': input_formats.NetworkInput(
        name = 'Wojtowicz2020',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        ncbi_tax_id = 9606,
        input = 'wojtowicz2020.wojtowicz2020_interactions',
        must_have_references = False,
        header = False,
        data_model = 'ligand_receptor',
    ),
    'cellchatdb-cofactors': input_formats.NetworkInput(
        name = 'CellChatDB-cofactors',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        sign = (4, 'stimulation', 'inhibition'),
        input = 'cellchatdb.cellchatdb_interactions',
        input_args = {'ligand_receptor': False},
        references = 6,
        header = False,
        must_have_references = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'ligand_receptor',
    ),
    'cellcall': input_formats.NetworkInput(
        name = 'CellCall',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = False,
        sign = False,
        input = 'cellcall.cellcall_interactions',
        input_args = {
            'extended': False,
        },
        must_have_references = False,
        header = False,
        data_model = 'ligand_receptor',
    ),
}


# synonym
ligrecextra = ligand_receptor


small_molecule_protein = {
    'signor': input_formats.NetworkInput(
        name = 'SIGNOR',
        separator = None,
        id_col_a = (0, lambda x: common.remove_prefix(x, ':')),
        id_col_b = (1, lambda x: common.remove_prefix(x, ':')),
        id_type_a = lambda line: (
            'pubchem'
                if common.is_str(line[0]) and line[0][:3] == 'CID' else
            'chebi'
                if common.is_str(line[0]) and line[0][:5] == 'CHEBI' else
            'uniprot'
        ),
        id_type_b = lambda line: (
            'pubchem'
                if common.is_str(line[1]) and line[1][:3] == 'CID' else
            'chebi'
                if common.is_str(line[1]) and line[1][:5] == 'CHEBI' else
            'uniprot'
        ),
        positive_filters = [
            (10, True), # only direct interactions
            lambda line: line[4] == 'chemical' or line[5] == 'chemical',
        ],
        entity_type_a = (
            4,
            {
                'chemical': 'small_molecule',
                'smallmolecule': 'small_molecule',
            }
        ),
        entity_type_b = (
            5,
            {
                'chemical': 'small_molecule',
                'smallmolecule': 'small_molecule',
            }
        ),
        is_directed = (
            6,
            [
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity by stabilization',
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
            ]
        ),
        sign = (
            6,
            [
                'up-regulates',
                'up-regulates activity',
                'up-regulates quantity by stabilization',
            ],
            [
                'down-regulates',
                'down-regulates activity',
                'down-regulates quantity by destabilization',
            ]
        ),
        input = 'signor.signor_interactions',
        references = (9, ';'),
        header = True,
        extra_edge_attrs = {
            'mechanism': (7, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'activity_flow',
        interaction_type = 'small_molecule_protein',
    ),
    # cancerdrugs_db format not yet done
    'cancerdrugsdb': input_formats.NetworkInput(
        name = 'CancerDrugsDB',
        separator = None,
        id_col_a = 0,
        id_col_b = 4,
        id_type_a = 'pubchem',
        id_type_b = 'uniprot',
        entity_type_a = 'small_molecule',
        entity_type_b = 'protein',
        ncbi_tax_id = {
            'A': _const.NOT_ORGANISM_SPECIFIC,
            'B': 9606,
        },
        is_directed = True,
        input = 'cancerdrugsdb.cancerdrugsdb_interactions',
        header = False,
        extra_edge_attrs = {},
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
        data_model = 'drug_target',
        interaction_type = 'small_molecule_protein',
    ),
    'cellinker': input_formats.NetworkInput(
        name = 'Cellinker',
        separator = None,
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'pubchem',
        id_type_b = 'uniprot',
        entity_type_a = 'small_molecule',
        entity_type_b = 'protein',
        ncbi_tax_id = 9606,
        is_directed = True,
        input = 'cellinker.cellinker_smol_interactions',
        references = (5, ';'),
        resource = (4, ';'),
        header = False,
        data_model = 'ligand_receptor',
        interaction_type = 'small_molecule_protein',
    ),
}

# synonym
small_molecule = small_molecule_protein


ligand_receptor['guide2pharma'] = copy.deepcopy(pathway['guide2pharma'])
ligand_receptor['guide2pharma'].must_have_references = False
ligand_receptor['icellnet'] = copy.deepcopy(pathway['icellnet'])
ligand_receptor['icellnet'].must_have_references = False
ligand_receptor['celltalkdb'] = copy.deepcopy(pathway['celltalkdb'])
ligand_receptor['celltalkdb'].must_have_references = False
ligand_receptor['cellchatdb'] = copy.deepcopy(pathway['cellchatdb'])
ligand_receptor['cellchatdb'].must_have_references = False
ligand_receptor['connectomedb'] = copy.deepcopy(pathway['connectomedb'])
ligand_receptor['connectomedb'].must_have_references = False
ligand_receptor['talklr'] = copy.deepcopy(pathway['talklr'])
ligand_receptor['talklr'].must_have_references = False
ligand_receptor['cellinker'] = copy.deepcopy(pathway['cellinker'])
ligand_receptor['cellinker'].must_have_references = False
ligand_receptor['scconnect'] = copy.deepcopy(pathway['scconnect'])
ligand_receptor['scconnect'].must_have_references = False

pathway['hpmr'] = copy.deepcopy(ligand_receptor['hpmr'])
pathway['hpmr'].must_have_references = True
pathway['hpmr'].positive_filters = []
pathway['cellphonedb'] = copy.deepcopy(ligand_receptor['cellphonedb'])
pathway['cellphonedb'].must_have_references = True
pathway['ramilowski2015'] = copy.deepcopy(ligand_receptor['ramilowski2015'])
pathway['ramilowski2015'].must_have_references = True
pathway['lrdb'] = copy.deepcopy(ligand_receptor['lrdb'])
pathway['lrdb'].must_have_references = True
pathway['baccin2019'] = copy.deepcopy(ligand_receptor['baccin2019'])
pathway['baccin2019'].must_have_references = True

"""
The default set of resources in OmniPath.
"""
omnipath = {}
omnipath.update(pathway)
omnipath.update(ptm)
omnipath.update(interaction)

del omnipath['netpath']
#del omnipath['innatedb']
del omnipath['alz']
omnipath['hprd'] = interaction_htp['hprd']
"""
Manually curated negative interactions, i.e. pairs of
proteins proved in experiments to not interact with
each other.
"""
negative = {
    'negatome': input_formats.NetworkInput(
        name = 'Negatome',
        separator = '\t',
        id_col_a = 0,
        id_col_b = 1,
        id_type_a = 'uniprot',
        id_type_b = 'uniprot',
        entity_type_a = 'protein',
        entity_type_b = 'protein',
        is_directed = 0,
        input = 'negatome_pairs',
        ncbi_tax_id = 9606,
        extra_edge_attrs = {
            'reference': (2, ';'),
            'method': (3, ';'),
        },
        extra_node_attrs_a = {},
        extra_node_attrs_b = {},
    ),
}

gdsc_comp_target = input_formats.NetworkInput(
    name = 'GDSC',
    separator = ';',
    id_col_a = 1,
    id_col_b = 0,
    id_type_a = 'pubchem',
    id_type_b = 'genesymbol',
    entity_type_a = 'drug',
    entity_type_b = 'protein',
    is_directed = 1,
    input = 'gdsc.sif',
    extra_edge_attrs = {},
    extra_node_attrs_a = {'gene_name': 2},
    extra_node_attrs_b = {},
)

cgc = input_formats.ReadList(
    name = 'cgc',
    id_col = 2,
    id_type = 'entrez',
    entity_type = 'protein',
    input = 'get_cgc',
    extra_attrs = {},
)

intogen_cancer = input_formats.ReadList(
    name = 'IntOGen',
    separator = '\t',
    id_col = 1,
    id_type = 'genesymbol',
    entity_type = 'protein',
    input = None,
    extra_attrs = {},
)

reactome_modifications = {
    'phosphorylated': ('phosphorylation', 'X'),
    'glycosylated': ('glycosylation', 'X'),
    'acetylated': ('acetylated', 'X'),
    'prenylated': ('prenylation', 'X'),
    'ubiquitinated': ('ubiquitination', 'X'),
    'myristoylated': ('myristoylation', 'X'),
    'hydroxylated': ('hydroxylation', 'X'),
    'acetylated residue': ('acetylation', 'X'),
    'palmitoylated residue': ('palmitoylation', 'X'),
    'sumoylated lysine': ('sumoylation', 'K'),
    'O-palmitoyl-L-threonine': ('palmitoylation', 'T'),
    'acetylated L-serine': ('acetylation', 'S'),
    'glycosylated residue': ('glycosylation', 'X'),
    'methylated L-arginine': ('methylation', 'R'),
    'ubiquitination': ('ubiquitination', 'X'),
    'phosphorylated residue': ('phosphorylation', 'X'),
    'O-phospho-L-threonine': ('phosphorylation', 'T'),
    'O-glycosyl-L-threonine': ('glycosylation', 'T'),
    'methylated L-lysine': ('methylation', 'K'),
    'myristoylated residue': ('myristoylation', 'X'),
    'N-myristoyl-glycine': ('myristoylation', 'G'),
    'O-palmitoyl-L-serine': ('palmitoylation', 'S'),
    'palmitoylated residue [residue = N]': ('palmitoylation', 'X'),
    'N-acetylated L-lysine': ('acetylation', 'K'),
    'O-glycosyl-L-serine': ('glycosylation', 'S'),
    'N-acetyl-L-methionine': ('acetylation', 'M'),
    'ubiquitinylated lysine': ('ubiquitination', 'K'),
    'S-farnesyl-L-cysteine': ('farnesylation', 'C'),
    'S-phospho-L-cysteine': ('phosphorylation', 'C'),
    'hydroxylated proline': ('hydroxylation', 'P'),
    'palmitoylated residue [residue = Y]': ('palmitoylation', 'Y'),
    'O4\'-phospho-L-tyrosine': ('phosphorylation', 'Y'),
    'O-phospho-L-serine': ('phosphorylation', 'S'),
    'O-phospho-L-threonine': ('phosphorylation', 'T'),
    '(2S,4R)-4-hydroxyproline': ('hydroxylation', 'P'),
    '(2S,3S)-3-hydroxyproline': ('hydroxylation', 'P'),
    'O5-galactosyl-L-hydroxylysine': ('galactosytlation', 'K'),
    '(2S,5R)-5-hydroxylysine': ('hydroxylation', 'K'),
    'O5-glucosylgalactosyl-L-hydroxylysine': ('glucosylgalactosylation', 'K'),
    'N4-glycosyl-L-asparagine': ('glycosylation', 'N'),
    'S-palmitoyl-L-cysteine': ('palmitoylation', 'C'),
    'N-myristoylglycine': ('myristoylation', 'G'),
    'half cystine': ('half cystine', 'C'),
    'S-geranylgeranyl-L-cysteine': ('geranylation', 'C'),
    'N6-acetyl-L-lysine': ('acetylation', 'K'),
    'N\'-formyl-L-kynurenine': ('formylation', 'W'),
    'Oxohistidine (from histidine)': ('oxo', 'H'),
    'dihydroxyphenylalanine (Phe)': ('dihydroxylation', 'F'),
    'glutamyl semialdehyde (Pro)': ('glutamylation', 'P'),
    'monohydroxylated asparagine': ('hydroxylation', 'N'),
    'monohydroxylated proline': ('hydroxylation', 'P'),
    'ubiquitinylated lysine': ('ubiquitination', 'K'),
    'N6,N6,N6-trimethyl-L-lysine': ('trimethylation', 'K'),
    'N6,N6-dimethyl-L-lysine': ('dimethylation', 'K'),
    'N6-myristoyl-L-lysine': ('myristoylation', 'K'),
    'sumoylated lysine': ('sumoylation', 'K'),
    'N6-methyl-L-lysine': ('methylation', 'K'),
    'omega-N-methyl-L-arginine': ('methylation', 'R'),
    'asymmetric dimethyl-L-arginine': ('dimethylation', 'R'),
    'symmetric dimethyl-L-arginine': ('dimethylation', 'R'),
    'O4\'-glucosyl-L-tyrosine': ('glycosylation', 'Y'),
    'N6-biotinyl-L-lysine': ('biotinylation', 'K'),
    'O-acetyl-L-serine': ('acetylation', 'S'),
    '1-thioglycine': ('thiolation', 'G'),
    'S-acetyl-L-cysteine': ('acetylation', 'C'),
    'N-acetyl-L-alanine': ('acetylation', 'A'),
    'S-methyl-L-cysteine': ('methylation', 'C'),
    'L-gamma-carboxyglutamic acid': ('carboxylation', 'Z'),
    '(2S,3R)-3-hydroxyaspartic acid': ('hydroxylation', 'D'),
    'O-fucosyl-L-threonine': ('fucosylation', 'T'),
    'O-fucosyl-L-serine': ('fucosylation', 'S'),
    'O-palmitoleyl-L-serine': ('palmitoylation', 'S'),
    '1-thioglycine (C-terminal)': ('thiolation', 'G'),
    'neddylated lysine': ('neddylation', 'K'),
    'N-palmitoyl-L-cysteine': ('palmitoylation', 'C'),
    'S-farnesyl-L-cysteine': ('farnesylation', 'C')
}