Table S2. The top-100 literature features with respect to the 8 HPO terms that have individual AUCs equal to or above 0.9 in the organ subontology.

Category	Tokens
proteins/protein complexes	cx32, kisspeptin, -308, t308, smn2, ns5, trap-positive, mpp+-induced, 1-methyl-4-phenylpyridinium, tnf-alpha-mediated, tnf-alpha-stimulated, tnf–mediated, ink4a/arf, ns4b, hmsh6, fukutin, cdtb, ns5b, apoai, tnf–stimulated, ns4a, tnf-alpha-, rhbmp-2, tnf-alpha-treated, frataxin, ki-ras, connexin32, tcdb, recql4, =-galcer, tyrosinase-related, hpms2, her4, cd40-cd40l, lmp2a, ryrs, mg2+-atpase, ews-fli1, abeta42, fancc, p40phox, her1, bdnf-induced, trap+, gfap-ir, daf-16/foxo, hdl3, -238, [tnf-alpha], cd40/cd40l, tnf–treated, anti-ngf, tep1, recq, nt-4, pfemp1, zo-2, nphp1, tnf-alpha-dependent, pomt1, igm-positive, apoa-ii, p110alpha, fancf, tbx4, anti-cd40l, igg
genes	hmsh2, cx26, fkrp, smn1, cln3, nphp4, mn1, nnt, apex2, akt-2
pathways	ras/raf/mek/erk, pi3k-akt-mtor
diseases/phenotypes	cmt1a, hnpp, hdl2, cln2, hpp, fmf, rtt, hnpcc, charcot-marie-tooth, amenorrhea, rett, anticardiolipin
misc.	sheldrick, shelxl97, bruker, farrugia, ortep-3, platon, shelxs97, spek, sgdid, wlds, caii, aoa, tdf, crysalis, wingx, amf

The union set of the top-100 literature features with respect to the 8 HPO terms that have individual AUCs equal to or above 0.9. It is composed of 107 unique tokens. The token “-308” and “t308” in the “proteins/protein complexes” category are due to mis-tokenization of “miR-308”. Similarly, “-238” in the same category is due to mis-tokenization of “BQ-23”. Also “=-galcer” in the same category originated from α-galcer and β-galcer due to mis-handling of UTF characters α and β.