Dear community
I hope this message finds you well. I would like to ask if anyone has been able to integrate a new database (http://www.phi-base.org ) for use with MEGAN. I am interested in testing this database for the specific search of pathogens, but I am not sure whether MEGAN supports this type of integration. In particular, I am uncertain if it is relatively straightforward to create the required mapping file in order to carry out the integration.
Thank you in advance for any guidance or experiences you can share.
Anupam
October 14, 2025, 11:04pm
2
Dear @jalcantara ,
If you could describe this database a bit more, I can look into adding support for it in MEGAN. I’d like to know whether it contains protein or nucleotide sequences , and whether your interest is mainly in pathogens or their related functions . It would also help to know if the database includes functional or taxonomic ontology information . With a brief explanation of these details, I can easily add support for it.
Best regards,
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Thank you once again for your help and for your contribution to both me and the community.
This database contains protein sequences, and I’m interested in using it for taxonomic and functional assignments related to pathogens. I understand that the database includes the following information:
Curation_comments_temp
to_do Record ID
PHI_MolConn_ID
IdentifierTypeOfProteinID
ProteinID
IdentifierTypeOfGeneLocusID
GeneLocusID
AA sequence #no EMBL#
NT sequence #no EMBL#
Genomic sequence providing strain
Gene_name
Genome location
Specific modification/s to the targeted protein or promoter
Accession ID for the modified genetic element
Known interacting protein(s) in the pathogen
Interacting protein - locus ID
Multiple_mutation
Pathogen_NCBI_species_Taxonomy ID
Pathogen_species
Pathogen_NCBI_strain_Taxonomy_ID
Experimental_strain
Disease_name
Host_descripton
Host_NCBI_Taxonomy_ID
Experimental_host_species
Host_strain_genotype_or cultivar_taxonomy_ID_NCBI
HostGenotype_definedGene of interest
HostGenotype_definedGene of interest _AccessionID
tissue_type
Function
GO_annotation
Database
Pathway_secretion_systems
Phenotype_of_mutant
Mating_defect_prior_to_penetration
Pre_penetration_defect
Penetration_defect
Post_penetration_defect
Disease_development_macroscopically_visible
Vegetative_spores
Sexual_spores
In_vitro_growth
Spore_germination
Essential_gene_Lethal_knockout
Inducer
ChemicalAccession (Chebi/CAS)
Tested Host_target
TestedHostTarget_AccessionID
Interaction phenotype
Host_response
Experimental_evidence
Transient Assay Experimental Evidence
Species_Expert
Entered_by
Literature_ID
Literature_source
DOI
Full_citation
Author_email
Comments
Reference
Year_published
Curation details
File_name_pdf_files_provided
batch_no Curation date
curator_organisation lab FG_mycotoxin Additional IdentifierTypeOfGeneLocusID
Additional GeneLocusID
Anti-infective (Chemical)
Compound
Target site
Group name
Chemical group
Mode in planta
Mode of action
FRAC CODE
Additional comments on anti-infectives
Curation Comments
To do
Record ID
PHI_MolConn_ID
Protein ID source
Protein ID
Gene ID source
Gene ID
AA sequence
NT sequence
Sequence Strain
Gene
Chr location
Gene/Protein modification
Modified gene/protein Id
Interacting partner(s)
Interacting partner(s) Id
Multiple mutation
Pathogen ID
Pathogen species
Pathogen strain ID
Pathogen strain
Disease
Host description
Host ID
Host species
Host strain
Host genotype
Host genotype-Id
Tissue
Gene Function
GO annotation
Database
Pathway
Mutant Phenotype
Mating defect
Prepenetration defect
Penetration defect
Postpenetration defect
Disease manifestation
Vegetative spores
Sexual spores
Invitro growth
Spore germination
Essential gene
Gene inducer
Gene inducer Id
Host target
Host target Id
Interaction phenotype
Host response
Exp. Technique-stable
Exp. Technique-transient
Species expert
Entered by
PMID
Ref. Source
DOI
Ref. detail
Author email
Comments
Author reference
Year
Curation details
File name
Batch no.
Curation date
Curator organization
Lab
FG-mycotoxin
AdditionalIdentifierTypeOfGeneLocusID
AdditionalGeneLocusID
Anti infective agent
Anti infective compound
Anti infective-target site
Anti infective group name
Anti infective Chemical group
Anti infective-Mode in planta
Mode of action
FRAC CODE
Anti infective-comments
Record 1
PHI:3
UniProt
P26215
EMBL
AAA79885
SB111
PGN1
5017
Bipolaris zeicola
SB111
leaf spot
monocots
4577
Zea mays (related: maize)
endopolygalacturonase
GO:0004650
GO
unaffected pathogenicity
no
no
no
pectin
gene disruption
MU; JA
2152162
PubMed
10.1105/tpc.2.12.1191
Expression during all infection stages. pathogen formerly called Cochliobolus carbonum teleomorph name
Scott-Craig et al.
1990
PHI-base Vers.3.3
2005-05-04
RRes
Record 2
PHI:7
UniProt
P22287
EMBL
CAA42824
race 5
AVR9
5499
Fulvia fulva
leaf mold
eudicots
4081
Solanum lycopersicum (related: tomato)
effector protein
effector (plant avirulence determinant)
gene deletion; gene complementation; biochemical evidence
MU
1799694
PubMed
no data found
Van Kan et al.
1991
PHI-base Vers.3.3
2005-05-04
RRes
Record 3
PHI:12
UniProt
Q01886
EMBL
AAA33023
SB111
HTS1
5017
Bipolaris zeicola
SB111
leaf spot
monocots
4577
Zea mays (related: maize)
cylic peptide synthase
GO:0009405, IMP
GO
loss of pathogenicity
gene disruption
TKB; JA
11607305
PubMed
no data found
pathogen formerly called Cochliobolus carbonum teleomorph name
Panaccione et al.
1992
PHI-base Vers.3.3
2005-05-04
RRes
Head of the FASTA database
A0A014N184#PHI:124318#Eng1#92637#Metarhizium_acridum#increased_virulence_(hypervirulence)Avr5#5499#Fulvia_fulva#effector (plant_avirulence_determinant)
Can I receive support about how to made this useful with MEGAN?
Thank you @Anupam
Anupam
October 17, 2025, 10:29pm
4
Dear @jalcantara ,
I’m currently working on this and just need to determine which format would best support use as an ontology or hierarchy.
Please feel free to DM me your email address so we can coordinate.
Best regards,
1 Like