source_id enabled source_label source_group module collection input_list fasta_file metadata_file options version citation notes status FUNGI true FUNGI fungi mod_I /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-I.AllOralsDB.fungi.v2026.198.tsv Fungi detected in the oral samples. enabled MICROEUK_ENTAMOEBA true ENTAMOEBA microeuks mod_I /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-I.AllOralsDB.entamoeba.v2026.198.tsv Proxy for Entamoeba gingivalis; E. gingivalis genome unavailable in NCBI therefore include genomes of other Entamoeba species. enabled VIRUSES_HUMAN true VIRUSES_HUMAN viruses mod_I /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-I.AllOralsDB.viruses_humans.v2026.198.tsv Viruses that infect humans and have been detected in oral samples (sources include data from https://viralzone.expasy.org/ and the Human Virus Database http://computationalbiology.cn/humanVirusBase/). enabled VIRUSES_FUNGAL_MICROEUK true VIRUSES_FUNGAL_MICROEUK viruses mod_I /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-I.AllOralsDB.viruses_microeuks.v2026.198.tsv Viruses that infect fungi and other microeukaryotes (sources Kinsella et al. and Keeler et al.) enabled VIRUSES_DIETARY true VIRUSES_DIETARY viruses mod_I /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-I.AllOralsDB.viruses_dietary.v2026.198.tsv Viruses infecting plants and tobacco products, detected in oral samples (sources include Aguado-García et al., Rivera-Gutierrez 2023 et al., and literature survey). enabled VIRUSES_HERVS true VIRUSES_HERVS viruses mod_II /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-II.AllOralsDB.viruses_HERVs.v2026.198.tsv lineage_taxid_override=206037 Viruses that are endogenous in the human genome (HERVs). enabled ALLERGENONLINE_V24 false ALLERGENS allergens mod_II /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-II.AllergenOnlineV24.v2026.215.tsv V24 10.1002/mnfr.201500769 Source: AllergenOnline v24 (118 proteins with PDB chain accessions currently omitted from final output). disabled HSP2 false HSP2 human_salivary mod_II /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-II.HSP2.0.v2026.198.tsv Downloaded manually June 18, 2026. HSP2.0 (https://salivaryproteome.org/salivary-protein) disabled MICROEUK_TTENAX true TTENAX microeuks mod_III /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Mpeyako2024.trichomonas.v2026.198.fasta /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Mpeyako2024.trichomonas.v2026.198.tsv Mpeyako_etal_2024 10.3389/fmicb.2024.1437572 Proteins identified and provided by Mpeyako et al. as Suppl Table 2 and Suppl Data 3). enabled OBELISKS_ORAL true OBELISKS_ORAL obelisks mod_III /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Zheludev2024.obelisks_ORAL.v2026.215.fasta /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Zheludev2024.obelisks_ORAL.v2026.198.tsv Zheludev_etal_2024 10.25740/WB363NT3637 Subset of proteins from protein calls for Obelisk genomes identified by Zheludev (their Supp Table 2), filtered and reviewed to include only Obelisk proteins from oral/oral-proximal datasets (27 of 11,581 pyrodigal ORFs). enabled DAIRY_DB true DAIRY food mod_III /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Dairy_DB.SUBSET-151.fasta /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Dairy_DB.SUBSET-151.tsv Hendy_2019 10.15124/589742eb-287a-4576-a00a-30df33d9f52c Proteins provided by Hendy et al. as curated dairy proteins, developed for their study of ancient dental calculus, Wilkin et al. 2020. enabled OBELISKS false OBELISKS obelisks mod_III /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Zheludev2024.obelisks.v2026.215.fasta /projects/academic/kmkauffm/kauffman/ZZ.daysDir/2026.214_maniFasta_AllOralsDB_flavor_builds/maniFasta-dev/99.prepackaged_inputs/MOD-III.Zheludev2024.obelisks.v2026.198.tsv Zheludev_etal_2024 10.25740/WB363NT3637 All protein calls for Obelisk genomes identified in Zheludev (their Supp Table 2). disabled HUMAN_C false HUMAN_C human mod_IV human_uniprot protein_set=canonical disabled HUMAN_CI true HUMAN_CI human mod_IV human_uniprot protein_set=canonical_isoform enabled HUMAN_CIT false HUMAN_CIT human mod_IV human_uniprot protein_set=canonical_isoform_trembl disabled HOMD_ORAL_A false HOMD_ORAL_A bacteria_archaea mod_IV HOMD genomic_refseq_version=V11.03;sites=oral;download=true V11.03 homd.org HOMD PROKKA proteomes filtered to oral body site disabled HOMD_ORAL_S false HOMD_ORAL_S bacteria_archaea mod_IV HOMD genomic_refseq_version=V11.03;sites=oral;download=true;rank=species V11.03 homd.org HOMD PROKKA proteomes filtered to oral body site, only include 1 representative genome from each oral species. disabled HOMD_ORAL_G true HOMD_ORAL_G bacteria_archaea mod_IV HOMD genomic_refseq_version=V11.03;sites=oral;download=true;rank=genus V11.03 homd.org HOMD PROKKA proteomes filtered to oral body site, only include 1 representative genome from each oral genus. enabled HOMD_ORAL_F false HOMD_ORAL_F bacteria_archaea mod_IV HOMD genomic_refseq_version=V11.03;sites=oral;download=true;rank=family V11.03 homd.org HOMD PROKKA proteomes filtered to oral body site, only include 1 representative genome from each oral family. disabled CRAP_CCP true CRAP contaminants mod_IV cRAP set=ccp 10.5281/ZENODO.15115102 Cambridge Centre for Proteomics cRAP set. enabled