Table 1.

Ambiguity of headwords for gene/protein names in SemCat

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

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.