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The Semantic Measures Library and Toolkit: fast
computation of semantic similarity and relatedness using
biomedical ontologies
Sébastien Harispe, Sylvie Ranwez, Stefan Janaqi, Jacky Montmain
To cite this version:
Sébastien Harispe, Sylvie Ranwez, Stefan Janaqi, Jacky Montmain. The Semantic Measures Library
and Toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.
Bioinformatics, Oxford University Press (OUP), 2014, 30 (5), pp.740-742.
�10.1093/bioinformat-ics/btt581�. �hal-01059329�
T h e s e m a nti c m e a s ur e s li br ar y a n d t o ol kit: f a st c o m p ut ati o n of
s e m a nti c si mil arit y a n d r el at e d n e s s u si n g bi o m e di c al o nt ol o gi e s
S e´b a sti e n H ari s p e *, S yl vi e R a n w e z, St ef a n J a n a qi a n d J a c k y M o nt m ai n
L GI 2 P/ E M A R e s e ar c h C e ntr e, Sit e E E RI E, P ar c S ci e ntifi q u e G. B e s s e, 3 0 0 3 5 Nıˆm e s c e d e x 1, Fr a n c e A s s o ci at e E dit or: M arti n Bi s h o p
A B S T R A C T
S u m m ar y: T h e s e m a nti c m e a s ur e s li br ar y a n d t o ol kit ar e r o b u st o p e s o ur c e a n d e a s y t o u s e s oft w ar e s ol uti o n s d e di c at e d t o s e m a n-ti c m e a s ur e s. T h e y c a n b e u s e d f or l ar g e- s c al e c o m p ut an-ti o n s a n d a n al y s e s of s e m a nti c si mil ariti e s b et w e e n t er m s/ c o n c e pt s d efi n e d i n t er mi n ol o gi e s a n d o nt ol o gi e s. T h e c o m p ari s o n of e ntiti e s ( e. g. g e n e s) a n n ot at e d b y c o n c e pt s i s al s o s u p p ort e d. A l ar g e c oll e cti o n of m e a s-ur e s i s a v ail a bl e. N ot li mit e d t o a s p e cifi c a p pli c ati o n c o nt e xt, t h e li br ar y a n d t h e t o ol kit c a n b e u s e d wit h v ari o u s c o ntr oll e d v o c a b ul ari e s a n d o nt ol o g y s p e cifi c ati o n s ( e. g. O p e n Bi o m e di c al O nt ol o g y, R e s o ur c e D e s cri pti o n Fr a m e w or k). T h e pr oj e ct t ar g et s b ot h d e si g n er s a n d pr a ctiti o n er s of s e m a nti c m e a s ur e s pr o vi di n g a J A V A li br ar y, a s w ell a s a c o m m a n d-li n e t o ol t h at c a n b e u s e d o n p er s o n al c o m p ut er s or c o m p ut er cl u st er s.
A v ail a bilit y a n d i m pl e m e nt ati o n: D o w nl o a d s, d o c u m e nt ati o n, t ut ori al s, e v al u ati o n a n d s u p p ort ar e a v ail a bl e at htt p:// w w w. s e m a n-ti c- m e a s ur e s-li br ar y. or g.
C o nt a ct: h ari s p e. s e b a sti e n @ g m ail. c o m
1 I N T R O D U C TIO N
Bi o m e di c al o nt ol o gi es pr o vi d e w ell-str u ct ur e d a n d c o ntr oll e d v o c a b ul ari es of s p e cifi c d o m ai ns, e. g. bi ol o gi c al pr o c ess es a n d cli ni c al h e alt h c ar e t er mi n ol o g y. T h e y ar e i n cr e asi n gl y us e d t o dri v e d at a i nt e gr ati o n, i nf or m ati o n r etri e v al, d at a a n n ot ati o ns a n d d e cisi o n s u p p ort, t o cit e a f e w ( St e v e ns et al. , 2 0 0 0). O pe n r e p osit ori es s u c h as t h e O p e n Bi o m e di c al O nt ol o g y ( O B O) F o u n dr y or Bi o P ort al ( S mit h et al. , 2 0 0 7 ; W h et z el et al. , 2 0 1 1 ) pr o vi d e a c c ess t o h u n dr e ds of bi o m e di c al o nt ol o gi es e x pr ess e d i n v ari o us f or m ats, e. g. R es o ur c e D es cri pti o n Fr a m e w or k ( R D F), O B O, W e b O nt ol o g y L a n g u a g e ( O W L). T h es e str u ct ur e d v o c a b ul ari es ar e us e d t o c h ar a ct eri z e e ntiti es t hr o u g h c o n c e pt u al a n n ot ati o ns. F or i nst a n c e, g e n es ( pr o d u cts) c a n b e a n n ot at e d b y G e n e O nt ol o g y ( G O) t er ms t o d efi n e t h eir m ol e c ul ar f u n cti o ns, t h eir c ell ul ar l o c ati o ns or t h e bi ol o gi c al pr o c ess es i n w hi c h t h e y ar e i n v ol v e d ( As h b ur n er et al. , 2 0 0 0). T h os e u n a m bi g u o us a n n o-t ao-ti o ns c a n, o-t h er ef or e, b e us e d o-t o q u er y l ar g e c oll e co-ti o ns of d ao-t a t a ki n g i nt o a c c o u nt t h e k n o wl e d g e d efi n e d i n t h e o nt ol o g y, i. e. pr a ctiti o n ers s e ar c hi n g f or g e n es a n n ot at e d t o ‘ n u cl e osi d e bi n d-i n g’ wd-ill als o r etrd-i e v e g e n es a n n ot at e d t o ‘ A T P bd-i n dd-i n g’, as t h e o nt ol o g y s p e cifi es t h at ‘ A T P bi n di n g’ is a s p e cifi c t y p e of ‘ n u cl e osi d e bi n di n g’. H o w e v er, i n s o m e c as es, e x a ct s e ar c h es
ar e t o o c o nstr ai ni n g, a n d w e s e ar c h f or e ntities t h at are si mil ar or r el at e d t o t he q uer y. S u c h a n i m pr ecise s e ar c h is b as e d o n i nf or m ati o n r etri e v al t ec h ni q ues t h at r e q uire a f u n cti o n t o esti-m at e w het her or n ot t w o e ntities are si esti-mil ar or r el at e d wit h r e g ar ds t o t heir c o nc e pt u al a n n ot ati o ns. T h er ef or e, t o e x pl oit o nt ol o gi es a n d c orres p o n di n g a n n ot ati o ns, s e m a nti c m e as ur es ar e r e q uir e d. T he y ai m t o c o m p are c o nc e pts b y t a ki n g i nt o acc o u nt t h e s e m a ntic s p ac e i n w hi c h t he y ar e d efi n e d. T he y c a n, t heref or e, b e use d t o ass ess t he de gr ee of li k e n ess of c o nce pts defi ne d i n o nt ol o gi es or b et wee n e ntiti es a n n ot at e d b y t h os e c o n-ce pts ( P es q uit a et al., 2 0 0 9).
A n i ncre asi n g n u m b er of al g orit h ms r el y o n s e m a ntic me as-ur es, f or i nst a nc e t o a n al yze ge nes b as e d o n t heir m ol ec ul ar f u n c-ti o ns ( S y et al., 2 0 1 2) or r el at e d dis e ases ( Li et al., 2 0 1 1). Se m a nti c m e as ur es c a n als o assist i n c o m p aris o ns of p atie nt r ec or ds, c h e mic al c o m p o u n ds, dis e ases or a n y e ntit y t h at c a n be c h ar acteri ze d b y u n a m bi g u o us t er ms or c o n ce pts d efi n e d i n o nt ol o gi es or t hes a uri.
N u mer o us c o m m u niti es are i n v ol ve d i n t he st u d y of s e m a nti c me as ur es ( e. g. bi oi nf or m atics, N at ur al L a n g u a ge Pr o cessi n g, artifi ci al i nt elli ge nc e a n d Se m a ntic W e b). O wi n g t o t heir p o p ul arit y, m a n y me as ur es h a v e be e n desi g n e d f or diff er e nt o nt ol o gi es a n d tre at me nts ( e. g. ge ne a n al ysis, i nf or m ati o n r e-tri e v al): a r ece nt s ur ve y disti n g uis he d t e ns of me as ures de di c at e d t o t he G O al o n e ( G u zzi et al., 2 0 1 2). H o w e ver, c o m m u niti es f oc usi n g o n ot her t y pes of a n n ot at e d e ntities ( e. g. p atie nt r ec or ds) als o be nefit t he or etic al fi n di n gs m a d e b y st u d yi n g me as-ur es i n ot her s pecific d o m ai ns s uc h as m olec ul ar bi ol o g y a n d vi ce vers a. Ne vert hel ess, m ost s oft w ar e s ol uti o ns r el at e d t o s e m a nti c me as ur es are d e v el o pe d f or a s pecific t er mi n ol o g y/ o nt ol o g y a n d o nl y f oc us o n a li mite d s et of me as ur es ( Fr o¨hlic h et al., 2 0 0 7; Li et al., 2 0 1 1; M cI n n es et al., 2 0 0 9; Y u et al., 2 0 1 0). T o f e d er at e eff orts r el at e d t o t he desi g n a n d a n al ysis of s e m a ntic m e as ur es a n d t o r es p o n d t o t he ne e d f or a ge neri c s oft w ar e t o ol de di c at e d t o t he m, w e d e vel o pe d t he s e m a nti c me as ur es li br ar y ( S M L). T his arti cl e pr es e nts its b e n efits f or t he c o m p ut ati o n of s e m a nti c me as ur es usi n g bi o- o nt ol o gi es.
2 T H E S M L A N D T O O L KI T
T h e S M L is a n e xt e nsi ve, effi ci e nt a n d g e n eric o p e n-s o urc e li br ar y de dic at e d t o t he c o m p ut ati o n, d e vel o p me nt a n d a n al ysis of s e m a nti c me as ur es. N u mer o us f u n cti o n aliti es pr o vi de d b y t he S M L ar e als o a v ail a bl e wit hi n t he S M L- T o ol kit, a c o m m a n d-li n e pr o gr a m t h at c a n b e use d b y n o n- de vel o pers t o e asil y c o m p ute s e m a ntic m e as ur es o n p ers o n al c o m p uters or c o m p uter cl usters. T h e S M L a n d t he t o ol kit ar e distri b ut e d u n der t he o p e n-s o ur ce * T o w h o m c orres p o n de nce s h o ul d be a d dress e d.
Ce CI L L lic e ns e ( c o m p ati ble wit h t he wi d el y use d G N U Ge n er al P u blic Li ce nse).
T h e S M L us es cr oss- pl atf or m J A V A pr o gr a mi n g l a n g u a ge versi o n 1. 7, w hi c h is a v ail a ble f or m ost o per ati n g s yste ms. It c a n b e us e d t o c o m p ute s e m a nti c si mil arities of c o nc e pts/ ter ms defi ne d i n str uct ur e d t er mi n ol o gi es a n d o nt ol o gi es. It c a n als o b e use d t o assess t he s e m a ntic si mil arit y of p airs of e ntities a n n ot at e d b y c o n ce pts, e. g. p atie nt r ec or ds a n n ot at e d b y gr o u ps of c o nc e pts, g e n es a n n ot at e d b y G O t er ms, P u b Me d arti cl es a n n ot at e d b y M e S H descri pt ors. C o nsi deri n g a p air of t er ms/ e ntiti es, t he li br ar y c o m p ut es a si mil arit y s c ore. D e vel o pers c a n, t heref or e, e asil y e m be d s o urce c o de r ef erri n g t o t he li br ar y t o c o m p ut e m e as ur es i n t heir o w n al g orit h ms a n d a p plic ati o ns. T h e li br ar y s u p p orts v ari o us o nt ol o g y f or m ats a n d s pe cifi c a-ti o ns ( e. g. O B O, R D F, O W L). S p ecific o nt ol o g y l o a ders ar e als o pr o vi de d t o h a n dl e wi del y use d bi o me di c al t er mi n ol o gi es s uc h as Me S H a n d S N O M E D Cli ni c al T er ms ( S N O M E D C T). C ust o m k n o wle d ge r e pr es e nt ati o n l o a d ers c a n als o be a d de d t o t he S M L. I n a d diti o n, l o w-l e v el a ccess t o t he li br ar y e n a bles de vel o p ers t o fi nel y c o ntr ol t he u n d erl yi n g gr a p h m o del ( o nt ol o g y) t o a p pl y s pe cifi c tre at me nts s o meti mes r e q uir e d f or t he c o m p ut ati o n of s e m a ntic me as ur es (e. g. tr a nsiti ve r e d ucti o n t o r e m o ve t a x o n o m-i c al r e d u n d a n cm-i es).
A l ar ge c oll ecti o n of s e m a nti c me as ur es is pr o vi de d o ut- of-t he-b o x — v ersi o n 0. 7 s u p p orts a he-b o ut 5 0 me as ur es r el yi n g o n differe nt str at e gi es. T h a n ks t o t he fi ne- gr ai ne d c o ntr ol pr o vi de d b y t he li br ar y, t his l e a ds t o a b o ut 1 5 0 0 s pecific me as ur e c o nfi g ur ati o ns t h at c a n be s pe cifi e d f or c o nt e xt-s pecifi c a p plic ati o ns. I n a d d-iti o n, t he al g orit h ms d e v el o pe d i n t he S M L pr o vi de t he d esi g ners of s e m a ntic me as ur es a n e xt e nsi ve A p pli c ati o n Pr o gr a m mi n g I nt erf ac e a n d fr a me w or k t o e asil y de vel o p, t est a n d e v al u at e ne w m e as ur es. M or e o v er, b ec a use of its ge neri c u n d erl yi n g gr a p h d at a m o del, s e m a nti c me as ures d e vel o p e d usi n g t he S M L will b e n efit a l ar ge a u di e nc e. T h ose m e as ur es ar e n ot r estrict e d t o a s pe cifi c o nt ol o g y, w hi c h is t he c as e wit h e xisti n g s oft w ar e s ol uti o ns, a n d c a n, t heref or e, b e us e d wit h t he v ari o us k n o wl e d ge r e pr es e nt ati o ns s u p p orte d b y t he li br ar y. F urt her m ore, t he S M L r elies o n a gr a p h m o d el c o m p ati bl e wit h t he Li n k e d D at a p ar a di g m. T his e n a bles S M L users t o t a ke a d v a nt a ge of t he gr o wi n g n u m b er of d at as ets p u blis h e d acc or di n g t o Li n ke d D at a a n d Se m a nti c W e b visi o ns, e. g. s ee Bi o 2 R D F i niti ati ve ( B elle a u et al., 2 0 0 8).
T h e S M L e n a bl es l ar ge-s c ale c o m p ut ati o ns a n d a n al ys es of s e m a ntic me as ur es. It s u p p orts m ulti-t hr e a d e d pr oc esses f or f ast p ar allel c o m p ut ati o n o n m ultic ore pr oc ess ors. T a ble 1 pr es e nts a r u n ni n g ti me c o m p aris o n bet w ee n t hr ee li br aries de di-c at e d t o t he G O a n d t he S M L ( det aile d pr ot odi-c ol, ass o di-ci at e d s o urce c o de a n d a d diti o n al e v al u ati o ns ar e pr o vi de d at htt p:// w w w.s e m a ntic- me as ur es-li br ar y.c o m/s ml/ p erf or m a nc e).
B ase d o n t he S M L, a n o p e s o urce t o ol kit e n a bl es n o n-de v el o pers t o b e n efit fr o m f u n cti o n aliti es pr o vi n-de d b y t he li br ar y t hr o u g h e as y t o use c o m m a n d-li ne s oft w are. T h e S M L- T o ol kit is hi g hl y t u n e a ble a n d e n a bl es c o nte xt-s pe cifi c c o nfi g ur ati o ns t o b e s pe cifi e d d e p e n di n g o n t he e x p eri m e nt perf or me d: k n o wle d g e b as e t o use ( o nt ol o gi es, a n n ot ati o ns), r e q uire d d at a pre pr ocess-i n g (e. g. t he r e m o v al of t a x o n o mocess-i c r e d u n d a ncocess-ies), m e as ur e c o nstr ai nts ( e. g. al g orit h mi c c o m ple xit y, i nf or m ati o n t o t a ke i nt o ac c o u nt), s et of q ueri es t o perf or m (i. e. c o nc e pt or e ntit y i de ntifiers) a n d ot her ( o pti o n al) p ar a met ers ( e. g. o ut p ut fil e,
c o m p uter r es o urces all o c at e d). Det aile d c o nfi g ur ati o ns c a n be s pecifie d usi n g a n e xt e nsi bl e m ar k- u p l a n g u a g e fil e. S pecifi c c o m-m a n d-li ne i nt erf a ces, c all e d pr ofil es , ar e als o d e v el o pe d t o e as e t he us e of t he S M L- T o ol kit i n s pecific use c as es, e. g. t o esti m at e t he si mil arit y of g e nes r e g ar di n g t heir G O t er m a n n ot ati o ns. S uc h pr ofil es c a n b e us e d t o hi de t he a d v a n ce d c a p a biliti es of t he li br ar y, a n d t heref or e i m pr o ve t h e e x p erie n ce f or us ers i nt er-est e d o nl y i n c o m p uti n g s e m a ntic m e as ur es i n a s pe cifi c c o nte xt of use (e. g. ge n e or dise as e a n al ysis). R el at e d s o ur ce c o de a n d iss ue tr a c k ers are a v ail a ble fr o m t he p u blic de di c at e d r e p osit or y. C o m m u nit y s u p p ort is als o pr o vi de d t o f acilit at e us a g e a n d e ns ur e i m pr o ve me nts of b ot h t he li br ar y a n d t he t o ol kit.
O pe n s o urce, ge neri c, effi ci e nt a n d hi g hl y t u ne a bl e, t he S M L a n d t he t o ol kit ar e n ot li mit e d t o a s pecific o nt ol o g y a n d c a n, t her ef or e, be use d i n a br o a d fiel d of a p plic ati o n, (scie ntifi c) pr oj ects a n d s oft w ar e s ol uti o ns [ e. g. H aris pe et al. ( 2 0 1 3), S y et al. ( 2 0 1 2)].
A C K N O W L E D G E M E N T
T he a ut h ors w o ul d li k e t o t h a n k S M L us ers a n d d e v el o pers f or t heir c o ntri b uti o ns t o t he pr oj ect.
F u n di n g : Fre n c h Life S ci e nc es a n d He alt hc ar e Alli a n ce ( A VI E S A N).
C o nflict of I nt er est : n o n e de cl ar e d. R E F E R E N C E S
As h b ur n er, M. et al. ( 2 0 0 0) G e n e o nt ol o g y: t o ol f or t h e u nifi c ati o n of bi ol o g y. T h e G e n e O nt ol o g y C o ns orti u m. N at. Ge net. , 2 5 , 2 5 – 2 9.
Bell e a u, F. et al. ( 2 0 0 8) Bi o 2 R D F: t o w ar ds a m as h u p t o b uil d bi oi nf or m atics k n o w-l e d ge s yste ms. J. Bi o m e d. I nf. , 4 1 , 7 0 6 – 7 1 6.
Fr o¨hlic h, H. et al. ( 2 0 0 7) G O Si m – a n R- p ac k a ge f or c o m p ut ati o n of i nf or m ati o n t he or etic G O si mil arities b et w ee n t er ms a n d g e n e pr o d u cts. B M C Bi oi nf or m ati cs , 8 , 1 6 6.
G uz zi, P. H. et al. ( 2 0 1 2) S e m a nti c si mil arit y a n al ysis of pr otei n d at a: assess m e nt wit h bi ol o gi c al f e at ures a n d iss u es. Briefi n gs Bi oi nf or m atics , 1 3 , 5 6 9 – 5 8 5. H aris p e, S. et al. ( 2 0 1 3) S e m a nti c me as ur es b as e d o n R D F pr oje cti o ns: a p plic ati o n
t o c o nte nt- b as e d re c o m me n d ati o n s yste ms. I n: O n t h e M ov e t o M e a ni n gf ul I nter n et S yste ms: O T M 2 0 1 3 C o nfere nc es. S pri n ger Berli n Hei d el ber g, Gr a z ( A ustri a), p p. 6 0 6 – 6 1 5.
Li,J. et al. ( 2 0 1 1) D O Si m: A n R p ac k a ge f or si mil arit y b et we e n dis e ases b as e d o n Dise as e O nt ol o g y. B M C Bi oi nf or m ati cs , 1 2 , 2 6 6.
T a bl e 1. R u n ni n g ti m es of t he g e n eric S M L a n d t hre e t o ols d e dic at e d t o t he G O T o ols 1 K 1 0 K 1 M 1 0 0 M F ast Se m Si ma 0 m 1 3. 3 6 0 m 1 6. 7 9 7 m 8. 1 4 X G O Si m X X X X G O S e m Si m 2 7 m 0 2. 6 6 X X X S M L 0 m 1 0. 0 1 0 m 1 1. 1 8 1 m 3 8. 8 7 1 3 3 m 2 7. 4 4 S M L p ar allel 0 m 9. 8 0 0 m 1 0. 2 4 0 m 4 7. 6 2 5 8 m
ahtt p://s o urc ef or ge. n et/ pr oj ects/f astse msi m/.
N ote: F o ur t ests h a v e b ee n p erf or m e d c o nsi deri n g r a n d o m s a m ples of ge ne p airs wit h fi xe d siz es (s ee c ol u m ns, K ¼ 1 0 3, M ¼ 1 0 6). S M L p ar allel c orres p o n ds t o t h e S M L c o nfi g ure d wit h f o ur t hre a ds. ‘ X’ s p ecifi es t h at t he pr o cess re q uire d 4 6 G o of R A M or t o o k 4 4 h.
M cI n n es, B. T. et al. ( 2 0 0 9) U M L S-I nterf ac e a n d U M L S- Si mil arit y: o pe n s o urc e s oft w are f or m e as uri n g p at hs a n d s e m a nti c si mil arit y. A MI A A n n u. S y m p. Pr o c. , 2 0 0 9 , 4 3 1 – 4 3 5.
P es q uit a, C. et al. ( 2 0 0 9) S e m a nti c si mil arit y i n bi o me dic al o nt ol o gies. P L o S C o m p ut. Bi ol. , 5 , 1 2.
S mit h, B. et al. ( 2 0 0 7) T h e O B O F o u n dr y: c o or di n at e d e v ol uti o n of o nt ol o gies t o s u p-p ort bi o me di c al d at a i nte gr ati o n. N at. Bi ote c h n ol. , 2 5 , 1 2 5 1 – 1 2 5 5.
Ste ve ns, R. et al. ( 2 0 0 0) O nt ol o g y- b as e d k n o wl e d ge r e prese nt ati o n f or bi oi nf or-m ati cs. Bri efi n gs Bi oi nf or or-m ati cs , 1 , 3 9 8 – 4 1 4.
S y, M.- F. et al. ( 2 0 1 2) User c e ntere d a n d o nt ol o g y b as e d i nf or m ati o n r etrie v al s yste m f or life s ci e n ces. B M C Bi oi nf or m atics , 1 3 (S u p pl. 1 ), S 4.
W hetz el, P. L. et al. ( 2 0 1 1) Bi o P ort al: e n h a n ce d f u ncti o n alit y vi a n e w W e b s er vic es fr o m t h e N ati o n al C e nter f or Bi o me dic al O nt ol o g y t o a cc ess a n d use o nt ol o gi es i n s oft w ar e a p pli c ati o ns. N ucleic A ci ds Res. , 3 9 , W 5 4 1 – W 5 4 5.
Y u, G. et al. ( 2 0 1 0) G O S e m Si m: a n R p ac k a ge f or me as uri n g s e m a ntic si mil arit y a m o n g G O ter ms a n d g e n e pr o d u cts. Bi oi nf or m atics , 2 6 , 9 7 6 – 9 7 8.
