Skip to main content

Table 1 Ambiguity of headwords for gene/protein names in SemCat

From: Identifying named entities from PubMed® for enriching semantic categories

Gene/protein Ambiguity Headwords
Yes No gene, protein, kinase, receptor, transporter, pseudogene, enzyme, peptide, polypeptide, glycoprotein, lipoprotein, symporter, antiporter, collagen, polyprotein, cotransporter, crystallin, lectin, globin, tubulin, oncogene, phosphoprotein, ferredoxin, opsin, antibody, porin, flavoprotein, homeobox, actin, adhesin, isoenzyme, integrin, lysozyme, chaperonin, globulin, ribonucleoprotein, immunoglobulin, isozyme, cadherin, transcript, myosin, apoprotein, cyclin, autoantigen, hemoglobin, spectrin, cytochrome, flagellin, tropomyosin, kinesin, adaptin, keratin, peroxiredoxin, pilin, chemokine, casein, catenin, ferritin, enkephalin, histone, giardin, interferon, albumin, trypsin, glutaredoxin, metallothionein, cyclophilin, proteolipid, mucin, vasopressin, proteoglycan
Ambiguous Low -ase (i.e. terms ending in “ase”), regulator, antigen, isoform, inhibitor, repressor, hormone, toxin, ras, carrier, suppressor, ligand, translocator, phosphate, thioredoxin, neurotoxin
  High Greek letters (e.g. alpha, beta,...), Roman numerals, short strings (e.g. psi, orf, ib,...), precursor, subunit, homolog, chain, factor, component, family, product, channel, activator, system, variant, chaperone, superfamily, molecule, pump, exchanger, element, sequence, resistance, construct, allergen, exporter, transducer, sensor, finger, modulator, effector, antiterminator, fusion, defective, antagonist, locus, wing, acid, receiver, para, cofactor, spot, tail, pigment, class, coma, exon, interactor, coactivator
  Rarely used content, percentage, gain, frame, length, ratio, response, yield, defect, fiber, resistant
No No region, domain, complex, form, fragment, binding, weight, transport, member, cell, containing, fluid, related, associated, syndrome, putative, biosynthesis, repeat, activity, segment, preparation, smear, subfamily, dependent, terminus, substrate, determinant, site, level, motif, specific, subtype, mrna, dna, synthesis, fibroblast, cdna, cluster, assembly, membrane, mutant, transmembrane, virus, terminal, group, hybrid, flip, urine, function, number, periplasmic, yield, rich, plasmid, rate, metabolism, fold
  1. For each term, either the last word or the word before a preposition was considered as a headword. The uniqueness and the ambiguity for being a gene/protein name were judged by an annotator.