2018-04-12 12:48:02 +02:00
{ "id" : "1410.0286" , "text" : " L A F - F a b r i c : a d a t a a n a l y s i s t o o l f o r L i n g u i s t i c A n n o t a t i o n F r a m e w o r k w i t h a n a p p l i c a t i o n t o t h e H e b r e w B i b l e D i r k R o o r d a \ u 2217 \ u 2217 \ u 2217 G i n o K a l k m a n \ u 2217 \ u 2217 \ u 2217 M a r t i j n N a a i j e r \ u 2217 \ u 2217 \ u 2217 A n d r e a s v a n C r a n e n b u r g h \ u 2217 \ u 2217 \ u 2217 \ u 2217 \ u 2217 \ u 2217 \ u 2217 \ u 2217 \ u 2217 d i r k . r o o r d a @ d a n s . k n a w . n l g . j . k a l k m a n @ v u . n l m . n a a i j e r @ v u . n l a n d r e a s . v a n . c r a n e n b u r g h @ h u y g e n s . k n a w . n l \ u 2217 D a t a A r c h i v i n g a n d N e t w o r k e d S e r v i c e s - R o y a l N e t h e r l a n d s A c a d e m y o f A r t s a n d S c i e n c e s , A n n a v a n S a k s e n l a a n 1 0 ; 2 5 9 3 H T D e n H a a g , N e t h e r l a n d s \ u 2 2 1 7 \ u 2 2 1 7 T h e L a n g u a g e A r c h i v e - M a x P l a n c k I n s t i t u t e f o r P s y c h o l i n g u i s t i c s , W u n d t l a a n 1 ; 6 5 2 5 X D N i j m e g e n , N e t h e r l a n d s a r X i v : 1 4 1 0 . 0 2 8 6 v 1 [ c s . C L ] 1 O c t 2 0 1 4 \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 E e p T a l s t r a C e n t r e f o r B i b l e a n d C o m p u t i n g - V U U n i v e r s i t y , F a c u l t e i t d e r G o d g e l e e r d h e i d ; D e B o e l e l a a n 1 1 0 5 ; 1 0 8 1 H V A m s t e r d a m , N e t h e r l a n d s \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 H u y g e n s I n s t i t u t e f o r t h e H i s t o r y o f t h e N e t h e r l a n d s - R o y a l N e t h e r l a n d s A c a d e m y o f A r t s a n d S c i e n c e s , P . O . b o x 9 0 7 5 4 ; 2 5 0 9 L T ; D e n H a a g , N e t h e r l a n d s \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 \ u 2 2 1 7 I n s t i t u t e f o r L o g i c L a n g u a g e a n d C o m p u t a t i o n - U n i v e r s i t y o f A m s t e r d a m , F N W I I L L C U n i v e r s i t e i t v a n A m s t e r d a m ; P . O . B o x 9 4 2 4 2 ; 1 0 9 0 G E A m s t e r d a m , N e t h e r l a n d s A b s t r a c t T h e L i n g u i s t i c A n n o t a t i o n F r a m e w o r k ( L A F ) p r o v i d e s a g e n e r a l , e x t e n s i b l e s t a n d - o f f m a r k u p s y s t e m f o r c o r p o r a . T h i s p a p e r d i s c u s s e s L A F - F a b r i c , a n e w t o o l t o a n a l y s e L A F r e s o u r c e s i n g e n e r a l w i t h a n e x t e n s i o n t o p r o c e s s t h e H e b r e w B i b l e i n p a r t i c u l a r . W e f i r s t w a l k t h r o u g h t h e h i s t o r y o f t h e H e b r e w B i b l e a s t e x t d a t a b a s e i n d e c e n n i u m - w i d e s t e p s . T h e n w e d e s c r i b e h o w L A F - F a b r i c m a y s e r v e a s a n a n a l y s i s t o o l f o r t h i s c o r p u s . F i n a l l y , w e d e s c r i b e t h r e e a n a l y t i c p r o j e c t s / w o r k f l o w s t h a t b e n e f i t f r o m t h e n e w L A F r e p r e s e n t a t i o n : 1 ) t h e s t u d y o f l i n g u i s t i c v a r i a t i o n : e x t r a c t c o o c c u r r e n c e d a t a o f c o m m o n n o u n s b e t w e e n t h e b o o k s o f t h e B i b l e ( M a r t i j n N a a i j e r ) ; 2 ) t h e s t u d y o f t h e g r a m m a r o f H e b r e w p o e t r y i n t h e P s a l m s : e x t r a c t c l a u s e t y p o l o g y ( G i n o K a l k m a n ) ; 3 ) c o n s t r u c t i o n o f a p a r s e r o f c l a s s i c a l H e b r e w b y D a t a O r i e n t e d P a r s i n g : g e n e r a t e t r e e s t r u c t u r e s f r o m t h e d a t a b a s e ( A n d r e a s v a n C r a n e n b u r g h ) . 1 . T h e H e b r e w B i b l e T h e H e b r e w B i b l e i s w r i t t e n i n o l d f o r m s o f H e b r e w a n d A r a m a i c , w h i c h a r e d e a d l a n g u a g e s n o w . W r i t t e n m a n u s c r i p t s a r e o u r o n l y s o u r c e f o r s t u d y i n g t h e s e l a n g u a g e s . T h e s t u d y o f s u c h a b o d y o f h i s t o r i c a l t e x t s i n v o l v e s r e s e a r c h q u e s t i o n s f r o m d i f f e r e n t d i s c i p l i n e s . L i n g u i s t i c a n a l y s i s i s a s t e p p i n g s t o n e w h i c h m u s t b e f o l l o w e d b y q u e s t i o n s a t h i g h e r l e v e l s o f a b s t r a c t i o n , s u c h a s l i t e r a r y q u e s t i o n s : h o w d i d a u t h o r s u s e t h e s y s t e m o f t h e l a n g u a g e t o c r a f t t h e i r d e s i g n : i . e . s t y l e , l i t e r a r y e f f e c t , f o c u s , a n d a l l t h o s e f e a t u r e s o f t h e t e x t t h a t a r e n o t d i c t a t e d b y t h e l a n g u a g e s y s t e m ( v a n P e u r s e n e t a l . 2 0 1 0 ) ? A n o t h e r l i n e o f q u e s t i o n s f a l l s i n t o h i s t o r i c a l l i n g u i s t i c s : s y s t e m a t i c a l l y c h a r t i n g l i n g u i s t i c v a r i a t i o n i n t h e b i b l i c a l l i n g u i s t i c c o r p u s c a n h e l p a d d r e s s i n g t h e q u e s t i o n a s t o w h e t h e r t h e v a r i a t i o n r e f l e c t s d i a c h r o n i c d e v e l o p m e n t ( v a n P e u r s e n a n d v a n K e u l e n 2 0 0 6 ) . 1 . 1 B i b l e a n d C o m p u t e r N a t u r a l l y , a r e s e a r c h p r o g r a m a s m e n t i o n e d a b o v e s e e k s t o e m p l o y d i g i t a l t o o l s . I n f a c t , a g r o u p o f r e s e a r c h e r s i n A m s t e r d a m s t a r t e d c o m p i l i n g a t e x t d a t a b a s e i n t h e 1 9 7 0 s : t h e W e r k g r o e p I n f o r m a t i c a V r i j e U n i v e r s i t e i t ( W I V U ) . T h i s r e s u l t e d i n a d a t a b a s e o f t e x t a n d m a r k u p , t h e s o - c a l l e d W I V U d a t a b a s e ( T a l s t r a a n d S i k k e l 2 0 0 0 ) , w h i c h b e c a m e w i d e l y k n o w n b e c a u s e i t b e c a m e i n c o r p o r a t e d i n B i b l e s t u d y s o f t w a r e p a c k a g e s . T h e W I V U m a r k u p i s b a s e d o n o b s e r v a b l e c h a r a c t e r i s t i c s o f t h e t e x t s a n d r e f r a i n s f r o m b e i n g c o m m i t t e d t o a p a r t i c u l a r l i n g u i s t i c t h e o r y o r f r a m e w o r k . T h e r e i s n o e x p l i c i t g r a m m a r t o w h i c h t h e m a r k e d - u p t e x t m a t e r i a l h a s t o c o n f o r m . O n e o f t h e c o n s e q u e n c e s i s t h a t t h e d a t a c a n n o t c o n v e n i e n t l y b e d e s c r i b e d i n o n e h i e r a r c h i c a l s t r u c t u r e , a l t h o u g h h i e r a r c h y p l a y s a r o l e . T h e r e a r e s e v e r a l , i n c o m p a t i b l e h i e r a r c h i e s i m p l i c i t i n t h e d a t a . I n t h e 1 9 9 0 s t h e g r o u n d w o r k h a s b e e n l a i d f o r a n a n a l y t i c a l t o o l o p e r a t i n g o n t h e W I V U d a t a . I n h i s P h D . t h e s i s , D o e d e n s ( 1 9 9 4 ) d e f i n e d a d a t a b a s e m o d e l a n d a p a i
{ "id" : "1501.01866" , "text" : " T h e H e b r e w B i b l e a s D a t a : L a b o r a t o r y S h a r i n g E x p e r i e n c e s D i r k R o o r d a \ u 2217 \ u 2217 \ u 2217 d i r k . r o o r d a @ d a n s . k n a w . n l \ u 2217 D a t a A r c h i v i n g a n d N e t w o r k e d S e r v i c e s - R o y a l N e t h e r l a n d s A c a d e m y o f A r t s a n d S c i e n c e s , A n n a v a n S a k s e n l a a n 1 0 ; 2 5 9 3 H T D e n H a a g , N e t h e r l a n d s \ u 2 2 1 7 T h e L a n g u a g e A r c h i v e - M a x P l a n c k I n s t i t u t e f o r P s y c h o l i n g u i s t i c s , W u n d t l a a n 1 ; 6 5 2 5 X D N i j m e g e n , N e t h e r l a n d s a r X i v : 1 5 0 1 . 0 1 8 6 6 v 1 [ c s . C L ] 8 J a n 2 0 1 5 A b s t r a c t T h e s y s t e m a t i c s t u d y o f a n c i e n t t e x t s i n c l u d i n g t h e i r p r o d u c t i o n , t r a n s m i s s i o n a n d i n t e r p r e t a t i o n i s g r e a t l y a i d e d b y t h e d i g i t a l m e t h o d s t h a t s t a r t e d t a k i n g o f f i n t h e 1 9 7 0 s . B u t h o w i s t h a t r e s e a r c h i n t u r n t r a n s m i t t e d t o n e w g e n e r a t i o n s o f r e s e a r c h e r s ? W e t e l l a s t o r y o f B i b l e a n d c o m p u t e r a c r o s s t h e d e c a d e s a n d t h e n p o i n t o u t t h e c u r r e n t c h a l l e n g e s : ( 1 ) f i n d i n g a s t a b l e d a t a r e p r e s e n t a t i o n f o r c h a n g i n g m e t h o d s o f c o m p u t a t i o n ; ( 2 ) s h a r i n g r e s u l t s i n i n t e r - a n d i n t r a - d i s c i p l i n a r y w a y s , f o r r e p r o d u c i b i l i t y a n d c r o s s - f e r t i l i z a t i o n . W e r e p o r t r e c e n t d e v e l o p m e n t s i n m e e t i n g t h e s e c h a l l e n g e s . T h e s c e n e i s t h e t e x t d a t a b a s e o f t h e H e b r e w B i b l e , c o n s t r u c t e d b y t h e E e p T a l s t r a C e n t r e f o r B i b l e a n d C o m p u t e r ( E T C B C ) , w h i c h i s s t i l l g r o w i n g i n d e t a i l a n d s o p h i s t i c a t i o n . W e s h o w h o w a s u b t l e m i x o f c o m p u t a t i o n a l i n g r e d i e n t s e n a b l e s c h o l a r s t o r e s e a r c h t h e t r a n s m i s s i o n a n d i n t e r p r e t a t i o n o f t h e H e b r e w B i b l e i n n e w w a y s : ( 1 ) a s t a n d a r d d a t a f o r m a t , L i n g u i s t i c A n n o t a t i o n F r a m e w o r k ( L A F ) ; ( 2 ) t h e m e t h o d s o f s c i e n t i f i c c o m p u t i n g , m a d e a c c e s s i b l e b y ( i n t e r a c t i v e ) P y t h o n a n d i t s a s s o c i a t e d e c o s y s t e m . A d d i t i o n a l l y , w e s h o w h o w t h e s e e f f o r t s h a v e c u l m i n a t e d i n t h e c o n s t r u c t i o n o f a n e w , p u b l i c l y a c c e s s i b l e s e a r c h e n g i n e S H E B A N Q , w h e r e t h e t e x t o f t h e H e b r e w B i b l e a n d i t s u n d e r l y i n g d a t a c a n b e q u e r i e d i n a s i m p l e , y e t p o w e r f u l q u e r y l a n g u a g e M Q L , a n d w h e r e t h o s e q u e r i e s c a n b e s a v e d a n d s h a r e d . 1 . I n t r o d u c t i o n T h e H e b r e w B i b l e i s a c o l l e c t i o n o f a n c i e n t t e x t s r e s u l t i n g f r o m a t e n - c e n t u r i e s l o n g t r a d i t i o n . I t i s o n e o f t h e m o s t s t u d i e d t e x t s i n h u m a n c u l t u r e . I n f o r m a t i o n p r o c e s s i n g b y m a c h i n e s i s l e s s t h a n t w o c e n t u r i e s o l d , b u t s i n c e i t s i n c e p t i o n i t s c a p a b i l i t i e s h a v e e v o l v e d i n a n e x p o n e n t i a l m a n n e r u p t i l l n o w ( G l e i c k 2 0 1 1 ) . W e a r e i n t e r e s t e d i n w h a t h a p p e n s w h e n t h e H e b r e w B i b l e a s a n o b j e c t o f s t u d y i s b r o u g h t u n d e r t h e s c o p e o f t h e c u r r e n t m e t h o d s o f i n f o r m a t i o n p r o c e s s i n g . T h e E e p T a l s t r a C e n t r e f o r B i b l e a n d C o m p u t i n g ( E T C B C ) f o r m e r l y k n o w n a s W e r k g r o e p I n f o r m a t i c a V r i j e U n i v e r s i t e i t ( W I V U ) , h a s b e e n i n v o l v e d i n j u s t t h i s s i n c e t h e 1 9 7 0 s a n d t h e i r m e m b e r s a r e d e d i c a t e d t o t h i s a p p r o a c h . T h e c o m b i n a t i o n o f a r e l a t i v e l y s t a b l e s e t o f d a t a a n d a r a p i d l y e v o l v i n g s e t o f m e t h o d s u r g e s f o r r e f l e c t i o n . A d d t o t h a t a g r o w i n g s e t o f a m b i t i o u s r e s e a r c h q u e s t i o n s , a n d i t b e c o m e s c l e a r t h a t n o t o n l y r e f l e c t i o n i s n e e d e d b u t a l s o a c t i o n . M e t h o d s f r o m c o m p u t a t i o n a l l i n g u i s t i c s a n d t h e w i d e r d i g i t a l h u m a n i t i e s a r e t o b e u s e d , h e n c e p e o p l e f r o m d i f f e r e n t d i s c i p l i n e s h a v e t o b e i n v o l v e d . H o w c a n t h e E T C B C s h a r e i t s d a t a a n d w a y o f w o r k i n g p r o d u c t i v e l y w i t h p e o p l e t h a t a r e u s e d t o a w i d e v a r i e t y o f c o m p u t a t i o n a l w a y s ? I n t h i s a r t i c l e w e t e l l a s t o r y o f r e f l e c t i o n a n d a c t i o n , a n d t h e c h a r a c t e r s a r e d a t a b a s e s , d a t a f o r m a t s , q u e r y l a n g u a g e s , a n n o t a t i o n s , c o m p u t e r l a n g u a g e s , a r c h i v e s , r e p o s i t o r i e s a n d s o c i a l m e d i a . T h i s s t o r y h a s a b e g i n n i n g i n F e b r u a r y 2 0 1 2 , w h e n a g r o u p o f b i b l i c a l s c h o l a r s c o n v e n e d a t t h e L o r e n t z c e n t e r a t L e i d e n f o r t h e w o r k s h o p B i b l i c a l S c h o l a r s h i p a n d H u m a n i t i e s C o m p u t i n g : D a t a T y p e s , T e x t , L a n g u a g e a n d I n t e r p r e t a t i o n ( R o o r d a e t a l . 2 0 1 2 ) . T h e y s e a r c h e d f o r n e w w a y s t o o b t a i n c o m p u t a t i o n a l t o o l s t h a t m a t c h e d t h e i r r e s e a r c h i n t e r e s t s . T h e a u t h o r w a s p a r t o f t h a t m e e t i n g a n d h a d p r e p a r e d a d e m o a p p l i c a t i o n : a q u e r y s a v e r . I t w a s a n a t t e m p t t o i m p r o v e t h e s h a r i n g o f k n o w l e d g e . I t i s a c r a f t t o w r i t e s u c c e s s f u l q u e r i e s f o r t h e E T C B C H e b r e w T e x t d a t a b a s e , a n d b y p u b l i s h i n g t h e i r q u e r i e s , r e s e a r c h e r s m i g h t t e a c h e a c h o t h e r h o w t o d o i t . I n t h e y e a r s t h a t f o l l o w e d , t h i s i d e a h a s m a t e r i a l i z e d a s t h e r e s u l t o f t h e S H E B A N Q p r o j e c t ( S y s t e m f o r H E B r e w t e x t : A N n o t a t i o n s f o r Q u e r i e s a n d m a r k u p ) , a c
{ "id" : "1501.06412" , "text" : " T h e A n a t o m y o f R e l e v a n c e T o p i c a l , S n i p p e t a n d P e r c e i v e d R e l e v a n c e i n S e a r c h R e s u l t E v a l u a t i o n \ u 0 2 d a A l e k s a n d r C h u k l i n M a a r t e n d e R i j k e U n i v e r s i t y o f A m s t e r d a m , A m s t e r d a m , T h e N e t h e r l a n d s a r X i v : 1 5 0 1 . 0 6 4 1 2 v 1 [ c s . I R ] 2 6 J a n 2 0 1 5 a . c h u k l i n , d e r i j k e @ u v a . n l A B S T R A C T C u r r e n t l y , t h e q u a l i t y o f a s e a r c h e n g i n e i s o f t e n d e t e r m i n e d u s i n g s o - c a l l e d t o p i c a l r e l e v a n c e , i . e . , t h e m a t c h b e t w e e n t h e u s e r i n t e n t ( e x p r e s s e d a s a q u e r y ) a n d t h e c o n t e n t o f t h e d o c u m e n t . I n t h i s w o r k w e w a n t t o d r a w a t t e n t i o n t o t w o a s p e c t s o f r e t r i e v a l s y s t e m p e r f o r m a n c e a f f e c t e d b y t h e p r e s e n t a t i o n o f r e s u l t s : r e s u l t a t t r a c t i v e n e s s ( \ u 2 0 1 c p e r c e i v e d r e l e v a n c e \ u 2 0 1 d ) a n d i m m e d i a t e u s e f u l n e s s o f t h e s n i p p e t s ( \ u 2 0 1 c s n i p p e t r e l e v a n c e \ u 2 0 1 d ) . P e r c e i v e d r e l e v a n c e m a y i n f l u e n c e d i s c o v e r a b i l i t y o f g o o d t o p i c a l d o c u m e n t s a n d s e e m i n g l y b e t t e r r a n k i n g s m a y i n f a c t b e l e s s u s e f u l t o t h e u s e r i f g o o d - l o o k i n g s n i p p e t s l e a d t o i r r e l e v a n t d o c u m e n t s o r v i c e - v e r s a . A n d r e s u l t i t e m s o n a s e a r c h e n g i n e r e s u l t p a g e ( S E R P ) w i t h h i g h s n i p p e t r e l e v a n c e m a y a d d t o w a r d s t h e t o t a l u t i l i t y g a i n e d b y t h e u s e r e v e n w i t h o u t t h e n e e d t o c l i c k t h o s e i t e m s . W e s t a r t b y m o t i v a t i n g t h e n e e d t o c o l l e c t d i f f e r e n t a s p e c t s o f r e l e v a n c e ( t o p i c a l , p e r c e i v e d a n d s n i p p e t r e l e v a n c e s ) a n d h o w t h e s e a s p e c t s c a n i m p r o v e e v a l u a t i o n m e a s u r e s . W e t h e n d i s c u s s p o s s i b l e w a y s t o c o l l e c t t h e s e r e l e v a n c e a s p e c t s u s i n g c r o w d s o u r c i n g a n d t h e c h a l l e n g e s a r i s i n g f r o m t h a t . C a t e g o r i e s a n d S u b j e c t D e s c r i p t o r s H . 3 . 3 [ I n f o r m a t i o n S t o r a g e a n d R e t r i e v a l ] : I n f o r m a t i o n S e a r c h a n d R e t r i e v a l 1 . I N T R O D U C T I O N F o r d e c a d e s t h e m a i n e v a l u a t i o n p a r a d i g m f o r s e a r c h e n g i n e s w a s t h e C r a n f i e l d m e t h o d o l o g y [ 7 ] . I n a t y p i c a l s e t t i n g o f a T R E C c o n f e r e n c e , t h e d o c u m e n t s a r e e v a l u a t e d b y h u m a n r a t e r s w h o a s s i g n r e l e v a n c e l a b e l s b a s e d o n t h e i r j u d g e m e n t a b o u t t h e r e l e v a n c e o f t h e d o c u m e n t t o t h e u s e r \ u 2 0 1 9 s t o p i c o f i n t e r e s t , e x p r e s s e d a s a q u e r y . A g r a d e d r e l e v a n c e s c a l e i s t y p i c a l l y u s e d w i t h t o p i c a l r e l e v a n c e l a b e l s r a n g i n g f r o m 0 t o 4 o r f r o m i r r e l e v a n t t o h i g h l y r e l e v a n t . 9 \ u 0 2 d a N o w a t G o o g l e S w i t z e r l a n d . C o p y r i g h t i s h e l d b y t h e a u t h o r / o w n e r ( s ) . S I G I R \ u 2 0 1 9 1 4 W o r k s h o p o n G a t h e r i n g E f f i c i e n t A s s e s s m e n t s o f R e l e v a n c e ( G E A R \ u 2 0 1 9 1 4 ) , J u l y 1 1 , 2 0 1 4 , G o l d C o a s t , Q u e e n s l a n d , A u s t r a l i a . T h e s e r e l e v a n c e l a b e l s c a n b e o b t a i n e d e i t h e r f r o m t r a i n e d e x p e r t s o r u s i n g a c r o w d s o u r c i n g a p p r o a c h . E i t h e r w a y , c a s e s o f d i s a g r e e m e n t h a v e t o b e a d d r e s s e d , a n d t h o s e a r e u s u a l l y t r e a t e d a s r a t e r s \ u 2 0 1 9 m i s t a k e s , b u t m a y a l s o a r i s e f r o m d i f f e r e n t i n t e r p r e t a t i o n s o f t h e u s e r i n t e n t o r t h e n o t i o n o f r e l e v a n c e . I n a t r a d i t i o n a l e v a l u a t i o n a p p r o a c h a s i n g l e r e l e v a n c e l a b e l i s c h o s e n f o r e a c h d o c u m e n t - t o p i c p a i r . T h e s e l a b e l s a r e t h e n a g g r e g a t e d t o S E R P - l e v e l q u a l i t y m e a s u r e s s u c h a s D C G [ 9 ] o r E R R [ 2 ] . B y u s i n g a d d i t i o n a l i n p u t s f r o m r a t e r s , w e c a n ( a ) r e f i n e t h e s e q u a l i t y m e a s u r e s a n d ( b ) b e t t e r u n d e r s t a n d t h e p e r f o r m a n c e o f r e t r i e v a l s y s t e m s . 2 . R E L A T E D W O R K T h e i d e a t o s e p a r a t e p e r c e i v e d a n d t o p i c a l r e l e v a n c e w a s s u g g e s t e d b y [ 3 ] w h i l e d e s i g n i n g t h e D B N c l i c k m o d e l . U n l i k e e a r l i e r c l i c k m o d e l s , i t s u g g e s t s t h a t t h e l i k e l i h o o d o f a u s e r c l i c k i n g a d o c u m e n t d e p e n d s n o t o n t h e t o p i c a l r e l e v a n c e o f t h e d o c u m e n t , b u t r a t h e r o n i t s p e r c e i v e d r e l e v a n c e , s i n c e t h e u s e r c a n o n l y j u d g e b a s e d o n t h e r e s u l t s n i p p e t . T h i s i d e a w a s l a t e r p i c k e d u p b y [ 1 2 ] w h o s h o w e d t h a t w h i l e t o p i c a l a n d p e r c e i v e d r e l e v a n c e a r e c o r r e l a t e d , t h e r e i s a n o t i c e a b l e d i s c r e p a n c y b e t w e e n t h e m . T h e y p e r f o r m e d a s i m u l a t e d e x p e r i m e n t b y m o d e l i n g t h e u s e r c l i c k p r o b a b i l i t y a n d s h o w e d t h a t t a k i n g i t i n t o a c c o u n t w o u l d l e a d t o s u b s t a n t i a l l y d i f f e r e n t o r d e r i n g o f t h e s y s t e m s p a r t i c i p a t i n g i n a T R E C W e b T r a c k . T h e i d e a t o s e p a r a t e o u t s n i p p e t r e l e v a n c e a p p e a r s a f t e r t h e i n t r o d u c t i o n o f g o o d a b a n d o n m e n t [ 1 0 ] : c a s e s w h e n u s e r s a b a n d o n a s e a r c h r e s u l t p a g e w i t h o u t c l i c k i n g a n y r e s u l t s a n d y e t t h e y a r e s a t i s f i e d . T h i s m a y b e d u e t o t h e S E R P b e i n g r i c h w i t h i n s t a n t a n s w e r s [ 4 ] , e . g . , a w e a t h e r w i d g e t o r a d i c t i o n a r y b o x , o r d u e t o t h e f a c t t h a t a q u e r y h a s a p r e c i s e i n f o r m a t i o n a l n e e d , t h a t c a n e a s i l y b e a n s w e r e d i n a r e s u l t s n i p p e t [ 5 ] . I n f a c t , a s w a s s h o w n b y [ 1 1 ] a b i g p o r t i o n
{ "id" : "oai:arXiv.org:1309.2788" , "text" : " T r a i n i n g i n D a t a C u r a t i o n a s S e r v i c e i n a F e d e r a t e d D a t a I n f r a s t r u c t u r e - t h e F r o n t O \ u f b 0 3 c e \ u 2013 B a c k O \ u f b 0 3 c e M o d e l I n g r i d D i l l o , R e n e v a n H o r i k , a n d A n d r e a S c h a r n h o r s t a r X i v : 1 3 0 9 . 2 7 8 8 v 1 [ c s . D L ] 1 1 S e p 2 0 1 3 D a t a A r c h i v i n g a n d N e t w o r k e d S e r v i c e s , A n n a v a n S a k s e n l a a n 1 0 , 2 5 9 3 H T T h e H a g u e , T h e N e t h e r l a n d s { i n g r i d . d i l l o , r e n e . v a n . h o r i k , a n d r e a . s c h a r n h o r s t } @ d a n s . k n a w . n l h t t p : //www.dans.knaw.nl Abstract. The increasing volume and importance of research data leads to the emergence of research data infrastructures in which data management plays an important role. As a consequence, practices at digital archives and libraries change. In this paper, we focus on a possible alliance between archives and libraries around training activities in data curation. We introduce a so-called FrontO\ufb03ce\u2013BackO\ufb03ce model and discuss experiences of its implementation in the Netherlands. In this model, an e\ufb03cient division of tasks relies on a distributed infrastructure in which research institutions (i.e., universities) use centralized storage and data curation services provided by national research data archives. The training activities are aimed at information professionals working at those research institutions, for instance as digital librarians. We describe our experiences with the course DataIntelligence4Librarians. Eventually, we re\ufb02ect about the international dimension of education and training around data curation and stewardship. Keywords: data curation, data management, training, data sharing, data archive, digital libraries, education, science policy, documentation 1 Introduction A research archive can be depicted as a safe haven for research data, carefully selected, documented and stored for future consultation. Accordingly, the core tasks of a data archivist could be imagined to be con\ufb01ned to proper documentation, and the care for material preservation. In short: \u201dOur service starts where others drop the data\u201d1 . The current practices of archivists seem to deviate from such an archetype to a large extent. This turn of tables can best be understood by a recall to the history of archival sciences. In general, for archives of research data the same principles hold as for any other archive. In 1898, in the handbook, one of the foundational texts in archival sciences [1], Muller, Feith, and Fruin describe the archive as an organic entirety whose function cannot be determined 1 Personal communication Henk Koning, former Technical Archivist at DANS 2 Dillo Fig. 1. The federated data infrastructure - a collaborative framework. Scheme designed by Peter Doorn based on the Collaborative Data Infrastructure as envisioned in [6, p. 31] . a priori. On the contrary, its function needs to be de\ufb01ned and rede\ufb01ned depending on the development of the institution (i.e., a board or government) whose selected traces it is obliged to archive. In other words, Muller et al. describe a co-evolution of the institution and its archive. This view applied to a research data archive, the corresponding institution is none other than the science system. From out this viewpoint, it is not surprising that the profound changes in scienti\ufb01c practice [2] and scholarly communication [3] in\ufb02uence the expectations placed on a data archive or, more speci\ufb01cally, a sustainable digital archive (Trusted Digital Repository). The changing modes of scholarly communication and practice alter the form and content of what is seen worth to be preserved. [5] Changing research practices require new negotiations on the division of labor. Who is responsible for setting up digital research infrastructures including virtual research environments - the information service providers such as Trusted Digital Repositories (TDRs) or the research institutions? Who takes care of the preparation of (meta)\u2013data and formats prior to archiving? Who should preserve software tools - the labs which developed them or the archive together with \u2019data\u2019 for which they have been developed? The
{ "id" : "oai:arXiv.org:1310.3370" , "text" : " T a l k i n g W i t h S c h o l a r s : D e v e l o p i n g a R e s e a r c h E n v i r o n m e n t f o r O r a l H i s t o r y C o l l e c t i o n s M a x K e m m a n 1 , S t e f S c a g l i o l a 1 , F r a n c i s k a d e J o n g 1 , 2 , a n d R o e l a n d O r d e l m a n 2 , 3 a r X i v : 1 3 1 0 . 3 3 7 0 v 1 [ c s . D L ] 1 2 O c t 2 0 1 3 1 3 E r a s m u s U n i v e r s i t y R o t t e r d a m , R o t t e r d a m , T h e N e t h e r l a n d s { k e m m a n , s c a g l i o l a } @ e s h c c . e u r . n l 2 U n i v e r s i t y o f T w e n t e , E n s c h e d e , T h e N e t h e r l a n d s f . m . g . d e j o n g @ u t w e n t e . n l N e t h e r l a n d s I n s t i t u t e f o r S o u n d a n d V i s i o n , H i l v e r s u m , T h e N e t h e r l a n d s r o r d e l m a n @ b e e l d e n g e l u i d . n l A b s t r a c t . S c h o l a r s a r e y e t t o m a k e o p t i m a l u s e o f O r a l H i s t o r y c o l l e c t i o n s . F o r t h e u p t a k e o f d i g i t a l r e s e a r c h t o o l s i n t h e d a i l y w o r k i n g p r a c t i c e o f r e s e a r c h e r s , p r a c t i c e s a n d c o n v e n t i o n s c o m m o n l y a d h e r e d t o i n t h e s u b f i e l d s i n t h e h u m a n i t i e s s h o u l d b e t a k e n i n t o a c c o u n t d u r i n g d e v e l o p m e n t . T o t h i s e n d , i n t h e O r a l H i s t o r y T o d a y p r o j e c t a r e s e a r c h t o o l f o r e x p l o r i n g O r a l H i s t o r y c o l l e c t i o n s i s d e v e l o p e d i n c l o s e c o l l a b o r a t i o n w i t h s c h o l a r l y r e s e a r c h e r s . T h i s p a p e r d e s c r i b e s f o u r s t a g e s o f s c h o l a r l y r e s e a r c h a n d t h e f i r s t s t e p s u n d e r t a k e n t o i n c o r p o r a t e r e q u i r e m e n t s o f t h e s e s t a g e s i n a d i g i t a l r e s e a r c h e n v i r o n m e n t . K e y w o r d s : O r a l H i s t o r y , s c h o l a r l y r e s e a r c h , u s e r - c e n t e r e d d e s i g n , e x p l o r a t i o n , r e s u l t p r e s e n t a t i o n , d a t a c u r a t i o n , w o r d c l o u d , v i s u a l f a c e t s 1 I n t r o d u c t i o n T h e d i g i t a l t u r n h a s p r o f o u n d l y i n f l u e n c e d h i s t o r i c a l c u l t u r e a n d h a s l e d t o a r i s e i n t h e c r e a t i o n o f a u d i o - v i s u a l a r c h i v e s w i t h p e r s o n a l n a r r a t i v e s , c o m m o n l y i d e n t i f i e d a s O r a l H i s t o r y . F o r t h e g e n e r a l p u b l i c , s e a r c h i n g t h e s e a r c h i v e s b y m a k i n g u s e o f s t a n d a r d s e a r c h t o o l s m a y b e s u f f i c i e n t . Y e t f o r s c h o l a r s , t h e f u l l v a l u e o f t h i s t y p e o f d a t a c a n n o t b e e x p l o i t e d o p t i m a l l y a s a v a i l a b l e t o o l s d o n o t e n a b l e s c h o l a r s t o e n g a g e w i t h t h e c o n t e n t f o r t h e p u r p o s e s o f r e s e a r c h . W h e n w o r k i n g w i t h a u d i o - v i s u a l c o n t e n t , t h e a v a i l a b i l i t y o f a n n o t a t i o n s i s k e y t o t h e p r o c e s s o f d i g g i n g u p i n t e r e s t i n g f r a g m e n t s . I n t h e p a s t y e a r s , a l o t o f e f f o r t h a s b e e n p u t i n t o o l s f o r c r e a t i n g m a n u a l a n n o t a t i o n s a n d g e n e r a t i n g a n n o t a t i o n s ( s e m i - ) a u t o m a t i c a l l y . B u t t o a c c e l e r a t e s c h o l a r l y r e s e a r c h , t o o l s a r e r e q u i r e d t h a t c a n t a k e a v a i l a b l e a n n o t a t i o n s l a y e r s a s i n p u t a n d p r o v i d e m e a n s f o r v i s u a l i z a t i o n , c o m p r e s s i o n a n d a g g r e g a t i o n o f t h e d a t a . T h u s a l l o w i n g t h e r e s e a r c h e r t o e x p l o r e a n d p r o c e s s t h e d a t a , b o t h a t f r a g m e n t - , i t e m - a n d c o l l e c t i o n - l e v e l . H o w e v e r , t o d e v e l o p s u c h d e d i c a t e d d a t a e x p l o r a t i o n t o o l s , t e c h n o l o g y s p e c i a l i s t s a n d r e s e a r c h e r s i n t h e h u m a n i t i e s h a v e t o e n g a g e i n a p r o c e s s o f m u t u a l u n d e r s t a n d i n g a n d j o i n t d e v e l o p m e n t . T a k i n g c a r e f u l l y i n t o a c c o u n t t h e s p e c i f i c s e t o f p r a c t i c e s a n d c o n v e n t i o n s c o m m o n l y a d h e r e d t o w i t h i n t h e s u b f i e l d s i n t h e h u m a n i t i e s i s a m i n i m u m r e q u i r e m e n t f o r t h e u p t a k e o f t h e t e c h n o l o g y i n t h e d a i l y w o r k i n g p r a c t i c e o f s c h o l a r s . I n t h i s p a p e r w e p r e s e n t a r e s e a r c h t o o l d e v e l o p e d i n c l o s e c o l l a b o r a t i o n w i t h s c h o l a r s t h a t e n a b l e s s e a r c h i n g a n d e x p l o r a t i o n o f a g g r e g a t e d , h e t e r o g e n e o u s O r a l H i s t o r y c o n t e n t . 2 F o u r s t a g e s o f s c h o l a r l y r e s e a r c h T h e u s e r i n t e r f a c e d e v e l o p m e n t i s b a s e d u p o n f o u r s t a g e s o f s c h o l a r l y r e s e a r c h t h a t w e r e d e f i n e d o n t h e b a s i s o f a n i n v e s t i g a t i o n o f u s e s c e n a r i o s r e p o r t e d i n [ 1 ] . E x p l o r a t i o n a n d s e l e c t i o n . I n t h e f i r s t s t a g e , t h e f o c u s i s o n t h e e x p l o r a t i o n a n d s e l e c t i o n o f o n e o r m o r e c o n t e n t s e t s w i t h i n a n a r c h i v e t h a t m a y b e s u i t a b l e f o r a d d r e s s i n g a c e r t a i n s c h o l a r l y i s s u e . T h e f i r s t s t e p s i n c o n t e n t e x p l o r a t i o n b y a r e s e a r c h e r o f t e n c o m e d o w n t o s e a r c h i n g f o r m a t e r i a l . R e s e a r c h s t a r t s w i t h t h e s e a r c h f o r n e w o r a d d i t i o n a l d a t a . T h i s s t a g e c a n g e t t h e f o r m o f p l a i n b r o w s i n g , b u t i t c a n a l s o b e s t r o n g l y p u r p o s e - d r i v e n , ( e . g . , c h e c k i n g d e t a i l s , s e a r c h i n g f o r c o m p l e m e n t a r y s o u r c e s ) , i t e m - o r i e n t e d ( e . g . , f i n d i n g t h e f i r s t i n t e r v i e w w i t h a s p e c i f i c p e r s o n ) , o r d i r e c t e d t o w a r d s p a t t e r n s i n a c o l l e c t i o n , i n w h i c h c a s e a n e n t i r e d a t a s e t i s t h e f o c u s o f a t t e n t i o n . E x p l o r a t i o n a n d i n v e s t i g a t i o n . O n c e t h e r e l e v a n t m a t e r i a l s h a v e b e e n i d e n t i f i e d , t h e f o c u s i n t h e n e x t s t a g e i s m o s t l y o n t h e f u r t h e r e x p l o r a t i o n o f t h e c o l l e c t e d m a t e r i a l s , t h e o r d e r i n g , c o m p a r i s o n ( b y i n d i v i d u a l r e s e a r c h e r s o r i n j o i n t e f f o r t s ) a n d a n a l y s i s , a n d
{ "id" : "oai:arXiv.org:1312.3393" , "text" : " a r X i v : 1312.3393 v 2 [ c s . L G ] 17 D e c 2013 R e l a t i v e U p p e r C o n f i d e n c e B o u n d f o r t h e K - A r m e d D u e l i n g B a n d i t P r o b l e m M a s r o u r Z o g h i I S L A , U n i v e r s i t y o f A m s t e r d a m , T h e N e t h e r l a n d s m . z o g h i @ u v a . n l S h i m o n W h i t e s o n I S L A , U n i v e r s i t y o f A m s t e r d a m , T h e N e t h e r l a n d s s . a . w h i t e s o n @ u v a . n l R e m i M u n o s I N R I A L i l l e - N o r d E u r o p e , V i l l e n e u v e d \ u 2 0 1 9 A s c q , F r a n c e r e m i . m u n o s @ i n r i a . f r M a a r t e n d e R i j k e I S L A , U n i v e r s i t y o f A m s t e r d a m , T h e N e t h e r l a n d s A b s t r a c t T h i s p a p e r p r o p o s e s a n e w m e t h o d f o r t h e K - a r m e d d u e l i n g b a n d i t p r o b l e m , a v a r i a t i o n o n t h e r e g u l a r K - a r m e d b a n d i t p r o b l e m t h a t o f f e r s o n l y r e l a t i v e f e e d b a c k a b o u t p a i r s o f a r m s . O u r a p p r o a c h e x t e n d s t h e U p p e r C o n f i d e n c e B o u n d a l g o r i t h m t o t h e r e l a t i v e s e t t i n g b y u s i n g e s t i m a t e s o f t h e p a i r w i s e p r o b a b i l i t i e s t o s e l e c t a p r o m i s i n g a r m a n d a p p l y i n g U p p e r C o n f i d e n c e B o u n d w i t h t h e w i n n e r a s a b e n c h m a r k . W e p r o v e a f i n i t e - t i m e r e g r e t b o u n d o f o r d e r O ( l o g t ) . I n a d d i t i o n , o u r e m p i r i c a l r e s u l t s u s i n g r e a l d a t a f r o m a n i n f o r m a t i o n r e t r i e v a l a p p l i c a t i o n s h o w t h a t i t g r e a t l y o u t p e r f o r m s t h e s t a t e o f t h e a r t . 1 . I n t r o d u c t i o n I n t h i s p a p e r , w e p r o p o s e a n d a n a l y z e a n e w a l g o r i t h m , c a l l e d R e l a t i v e U p p e r C o n f i d e n c e B o u n d ( R U C B ) , f o r t h e K - a r m e d d u e l i n g b a n d i t p r o b l e m ( Y u e e t a l . , 2 0 1 2 ) , a v a r i a t i o n o n t h e K - a r m e d b a n d i t p r o b l e m , w h e r e t h e f e e d b a c k c o m e s i n t h e f o r m o f p a i r w i s e p r e f e r e n c e s . W e a s s e s s t h e p e r f o r m a n c e o f t h i s a l g o r i t h m u s i n g o n e o f t h e m a i n c u r r e n t a p p l i c a t i o n s o f t h e K - a r m e d d u e l i n g b a n d i t p r o b l e m , r a n k e r e v a l u a t i o n ( H o f m a n n e t a l . , 2 0 1 3 ; J o a c h i m s , 2 0 0 2 ; Y u e & J o a c h i m s , 2 0 1 1 ) , w h i c h i s u s e d i n i n f o r m a t i o n r e t r i e v a l , a d p l a c e m e n t a n d r e c o m m e n d e r s y s t e m s , a m o n g o t h e r s . d e r i j k e @ u v a . n l T h e K - a r m e d d u e l i n g b a n d i t p r o b l e m i s p a r t o f t h e g e n e r a l f r a m e w o r k o f p r e f e r e n c e l e a r n i n g ( F \ u 0 0 a 8 u r n k r a n z & H \ u 0 0 a 8 u l l e r m e i e r , 2 0 1 0 ; F \ u 0 0 a 8 u r n k r a n z e t a l . , 2 0 1 2 ) , w h e r e t h e g o a l i s t o l e a r n , n o t f r o m r e a l - v a l u e d f e e d b a c k , b u t f r o m r e l a t i v e f e e d b a c k , w h i c h s p e c i f i e s o n l y w h i c h o f t w o a l t e r n a t i v e s i s p r e f e r r e d . D e v e l o p i n g e f f e c t i v e p r e f e r e n c e l e a r n i n g m e t h o d s i s i m p o r t a n t f o r d e a l i n g w i t h d o m a i n s i n w h i c h f e e d b a c k i s n a t u r a l l y q u a l i t a t i v e ( e . g . , b e c a u s e i t i s p r o v i d e d b y a h u m a n ) a n d s p e c i f y i n g r e a l - v a l u e d f e e d b a c k i n s t e a d w o u l d b e a r b i t r a r y o r i n e f f i c i e n t ( F \ u 0 0 a 8 u r n k r a n z e t a l . , 2 0 1 2 ) . O t h e r a l g o r i t h m s p r o p o s e d f o r t h i s p r o b l e m a r e I n t e r l e a v e d F i l t e r ( I F ) ( Y u e e t a l . , 2 0 1 2 ) , B e a t t h e M e a n ( B T M ) ( Y u e & J o a c h i m s , 2 0 1 1 ) , a n d S A V A G E ( U r v o y e t a l . , 2 0 1 3 ) . A l l o f t h e s e m e t h o d s w e r e d e s i g n e d f o r t h e f i n i t e - h o r i z o n s e t t i n g , i n w h i c h t h e a l g o r i t h m r e q u i r e s a s i n p u t t h e e x p l o r a t i o n h o r i z o n , T , t h e t i m e b y w h i c h t h e a l g o r i t h m n e e d s t o p r o d u c e t h e b e s t a r m . T h e a l g o r i t h m i s t h e n j u d g e d b a s e d u p o n e i t h e r t h e a c c u r a c y o f t h e r e t u r n e d b e s t a r m o r t h e r e g r e t a c c u m u l a t e d i n t h e e x p l o r a t i o n p h a s e . 1 A l l t h r e e o f t h e s e a l g o r i t h m s u s e t h e e x p l o r a t i o n h o r i z o n t o s e t t h e i r i n t e r n a l p a r a m e t e r s , s o f o r e a c h T , t h e r e i s a s e p a r a t e a l g o r i t h m I F T , B T M T a n d S A V A G E T . B y c o n t r a s t , R U C B d o e s n o t r e q u i r e t h i s i n p u t , m a k i n g i t m o r e u s e f u l i n p r a c t i c e , s i n c e a g o o d e x p l o r a t i o n h o r i z o n i s o f t e n d i f f i c u l t t o g u e s s . N o n e t h e l e s s , R U C B o u t p e r f o r m s t h e s e a l g o r i t h m s i n t e r m s o f t h e a c c u r a c y a n d r e g r e t m e t r i c s u s e d i n t h e f i n i t e - h o r i z o n s e t t i n g . T h e m a i n i d e a o f R U C B i s t o m a i n t a i n o p t i m i s t i c e s t i m a t e s o f t h e p r o b a b i l i t i e s o f a l l p o s s i b l e p a i r w i s e o u t 1 T h e s e t e r m s a r e f o r m a l i z e d i n S e c t i o n 2 . R e l a t i v e U p p e r C o n f i d e n c e B o u n d c o m e s , a n d ( 1 ) u s e t h e s e e s t i m a t e s t o s e l e c t a p o t e n t i a l c h a m p i o n , w h i c h i s a n a r m t h a t h a s a c h a n c e o f b e i n g t h e b e s t a r m , a n d ( 2 ) s e l e c t a n a r m t o c o m p a r e t o t h i s p o t e n t i a l c h a m p i o n b y p e r f o r m i n g r e g u l a r U p p e r C o n f i d e n c e B o u n d ( A u e r e t a l . , 2 0 0 2 ) r e l a t i v e t o i t . W e p r o v e a f i n i t e - t i m e h i g h - p r o b a b i l i t y b o u n d o f O ( l o g t ) o n t h e c u m u l a t i v e r e g r e t o f R U C B , f r o m w h i c h w e d e d u c e a b o u n d o n t h e e x p e c t e d c u m u l a t i v e r e g r e t . T h e s e b o u n d s r e l y o n s u b s t a n t i a l l y l e s s r e s t r i c t i v e a s s u m p t i o n s o n t h e K - a r m e d d u e l i n g b a n d i t p r o b l e m t h a n I F a n d B T M a n d h a v e b e t t e r m u l t i p l i c a t i v e c o n s t a n t s t h a n t h o s e o f S A V A G E . F u r t h e r m o r e , o u r b o u n d s a r e t h e f i r s t e x p l i c i t l y n o n - a s y m p t o t i c r e s u l t s f o r t h e K - a r m e d d u e l i n g b a n
2018-04-18 17:00:21 +02:00
{ "id" : "oai:arXiv.org:1312.4428" , "text" : " O n C o n s t r a i n t S a t i s f a c t i o n P r o b l e m s b e l o w P \ u 2217 a r X i v : 1312.4428 v 2 [ c s . C C ] 17 D e c 2013 L \ u 0 0 b 4 a s z l \ u 0 0 b 4 o E g r i \ u 2020 A b s t r a c t S y m m e t r i c D a t a l o g , a f r a g m e n t o f t h e l o g i c p r o g r a m m i n g l a n g u a g e D a t a l o g , i s c o n j e c t u r e d t o c a p t u r e a l l c o n s t r a i n t s a t i s f a c t i o n p r o b l e m s ( C S P ) i n L . T h e r e f o r e d e v e l o p i n g t o o l s t h a t h e l p u s u n d e r s t a n d w h e t h e r o r n o t a C S P c a n b e d e f i n e d i n s y m m e t r i c D a t a l o g i s a n i m p o r t a n t t a s k . I t i s w i d e l y k n o w n t h a t a C S P i s d e f i n a b l e i n D a t a l o g a n d l i n e a r D a t a l o g i f a n d o n l y i f t h a t C S P h a s b o u n d e d t r e e w i d t h a n d b o u n d e d p a t h w i d t h d u a l i t y , r e s p e c t i v e l y . I n t h e c a s e o f s y m m e t r i c D a t a l o g , B u l a t o v , K r o k h i n a n d L a r o s e a s k f o r s u c h a d u a l i t y ( 2 0 0 8 ) . W e p r o v i d e t w o s u c h d u a l i t i e s , a n d g i v e a p p l i c a t i o n s . I n p a r t i c u l a r , w e g i v e a s h o r t a n d s i m p l e n e w p r o o f o f t h e r e s u l t o f D a l m a u a n d L a r o s e t h a t \ u 2 0 1 c M a l t s e v + D a t a l o g \ u 2 1 d 2 s y m m e t r i c D a t a l o g \ u 2 0 1 d ( 2 0 0 8 ) . I n t h e s e c o n d p a r t o f t h e p a p e r , w e p r o v i d e s o m e e v i d e n c e f o r t h e c o n j e c t u r e o f D a l m a u ( 2 0 0 2 ) t h a t e v e r y C S P i n N L i s d e f i n a b l e i n l i n e a r D a t a l o g . O u r r e s u l t s a l s o s h o w t h a t a w i d e c l a s s o f C S P s \ u 2 0 1 3 C S P s w h i c h d o n o t h a v e b o u n d e d p a t h w i d t h d u a l i t y ( e . g . , t h e P - c o m p l e t e H o r n - 3 S a t p r o b l e m ) \ u 2 0 1 3 c a n n o t b e d e f i n e d b y a n y p o l y n o m i a l s i z e f a m i l y o f m o n o t o n e r e a d - o n c e n o n d e t e r m i n i s t i c b r a n c h i n g p r o g r a m s . 1 I n t r o d u c t i o n C o n s t r a i n t s a t i s f a c t i o n p r o b l e m s ( C S P ) c o n s t i t u t e a u n i f y i n g f r a m e w o r k t o s t u d y v a r i o u s c o m p u t a t i o n a l p r o b l e m s a r i s i n g n a t u r a l l y i n v a r i o u s b r a n c h e s o f c o m p u t e r s c i e n c e , i n c l u d i n g a r t i f i c i a l i n t e l l i g e n c e , g r a p h h o m o m o r p h i s m s , a n d d a t a b a s e t h e o r y . L o o s e l y s p e a k i n g , a n i n s t a n c e o f a C S P c o n s i s t s o f a l i s t o f v a r i a b l e s a n d a s e t o f c o n s t r a i n t s , e a c h s p e c i f i e d b y a n o r d e r e d t u p l e o f v a r i a b l e s a n d a c o n s t r a i n t r e l a t i o n o v e r s o m e s p e c i f i e d d o m a i n . T h e g o a l i s t h e n t o d e t e r m i n e w h e t h e r v a r i a b l e s c a n b e a s s i g n e d d o m a i n v a l u e s s u c h t h a t a l l c o n s t r a i n t s a r e s i m u l t a n e o u s l y s a t i s f i e d . R e c e n t e f f o r t s h a v e b e e n d i r e c t e d a t c l a s s i f y i n g t h e c o m p l e x i t y o f t h e s o - c a l l e d n o n u n i f o r m C S P . F o r a f i x e d f i n i t e s e t o f f i n i t e r e l a t i o n s \ u 0 3 9 3 , C S P ( \ u 0 3 9 3 ) d e n o t e s t h e n o n u n i f o r m C S P c o r r e s p o n d i n g t o \ u 0 3 9 3 . T h e d i f f e r e n c e b e t w e e n a n i n s t a n c e o f C S P ( \ u 0 3 9 3 ) a n d a n i n s t a n c e o f t h e g e n e r a l C S P i s t h a t c o n s t r a i n t s i n a n i n s t a n c e o f C S P ( \ u 0 3 9 3 ) t a k e t h e f o r m ( x i 1 , . . . , x i k ) \ u 2 2 0 8 R f o r s o m e R \ u 2 2 0 8 \ u 0 3 9 3 . E x a m p l e s o f n o n u n i f o r m C S P s i n c l u d e k - S a t , H o r n - 3 S a t , G r a p h H - C o l o r i n g , a n d m a n y o t h e r s . \ u 2 2 1 7 R e s e a r c h s u p p o r t e d b y N S E R C , F Q R N T , a n d E R C S t a r t i n g G r a n t P A R A M T I G H T ( N o . 2 8 0 1 5 2 ) . I n s t i t u t e f o r C o m p u t e r S c i e n c e a n d C o n t r o l , H u n g a r i a n A c a d e m y o f S c i e n c e s ( M T A S Z T A K I ) , B u d a p e s t , H u n g a r y . { l a s z l o . e g r i @ m a i l . m c g i l l . c a } \ u 2020 1 F o r a r e l a t i o n a l s t r u c t u r e B , t h e h o m o m o r p h i s m p r o b l e m H O M ( B ) t a k e s a s t r u c t u r e A a s i n p u t , a n d t h e t a s k i s t o d e t e r m i n e i f t h e r e i s a h o m o m o r p h i s m f r o m A t o B . F o r i n s t a n c e , c o n s i d e r s t r u c t u r e s t h a t c o n t a i n a s i n g l e s y m m e t r i c b i n a r y r e l a t i o n , i . e . , g r a p h s . A h o m o m o r p h i s m f r o m a g r a p h G t o a g r a p h H i s a m a p p i n g f r o m V G t o V H s u c h t h a t a n y e d g e o f G i s m a p p e d t o a n e d g e o f H . I f H i s a g r a p h w i t h a s i n g l e e d g e t h e n H O M ( H ) i s t h e s e t o f g r a p h s w h i c h a r e t w o - c o l o r a b l e . T h e r e i s a w e l l - k n o w n a n d s t r a i g h t f o r w a r d c o r r e s p o n d e n c e b e t w e e n t h e C S P a n d t h e h o m o m o r p h i s m p r o b l e m . F o r t h i s r e a s o n , f r o m n o w o n w e w o r k o n l y w i t h t h e h o m o m o r p h i s m p r o b l e m i n s t e a d o f t h e C S P . N e v e r t h e l e s s , w e c a l l H O M ( B ) a C S P a n d w e a l s o w r i t e C S P ( B ) i n s t e a d o f H O M ( B ) , a s i t i s o f t e n d o n e i n t h e l i t e r a t u r e . T h e C S P i s o f c o u r s e N P - c o m p l e t e , a n d t h e r e f o r e r e s e a r c h h a s f o c u s e d o n i d e n t i f y i n g \ u 201 c i s l a n d s \ u 201 d o f t r a c t a b l e C S P s . T h e w e l l - k n o w n C S P d i c h o t o m y c o n j e c t u r e o f F e d e r a n d V a r d i [ 13 ] s t a t e s t h a t e v e r y C S P i s e i t h e r t r a c t a b l e o r N P - c o m p l e t e , a n d p r o g r e s s t o w a r d s t h i s c o n j e c t u r e h a s b e e n s t e a d y d u r i n g t h e l a s t f i f t e e n y e a r s . F r o m a c o m p l e x i t y - t h e o r e t i c p e r s p e c t i v e , t h e c l a s s i f i c a t i o n o f C S P ( B ) a s i n P o r b e i n g N P - c o m p l e t e i s r a t h e r c o a r s e a n d t h e r e f o r e s o m e w h a t d i s s a t i s f a c t o r y . C o n s e q u e n t l y , u n d e r s t a n d i n g t h e f i n e - g r a i n e d c o m p l e x i t y o f C S P s g a i n e d c o n s i d e r a b l e a t t e n t i o n d u r i n g t h e l a s t f e w y e a r s . U l t i m a t e l y , o n e w o u l d l i k e t o k n o w t h e p r e c i s e c o m p l e x
{ "id" : "Clusa-et-al.2016.PlosOne" , "text" : " R E S E A R C H A R T I C L E A n E a s y P h y l o g e n e t i c a l l y I n f o r m a t i v e M e t h o d t o T r a c e t h e G l o b a l l y I n v a s i v e P o t a m o p y r g u s M u d S n a i l f r o m R i v e r ’ s e D N A L a u r a C l u s a 1 * , A l b a A r d u r a 2 , F i o n a G o w e r 3 , L a u r a M i r a l l e s 1 , V a l e n t i n a T s a r t s i a n i d o u 1 , A n a s t a s i j a Z a i k o 3 , 4 , E v a G a r c i a - V a z q u e z 1 1 D e p a r t m e n t o f F u n c t i o n a l B i o l o g y , U n i v e r s i t y o f O v i e d o , C / J u l i a n C l a v e r i a s / n 3 3 0 0 6 , O v i e d o , S p a i n , 2 U S R 3 2 7 8 - C R I O B E - C N R S - E P H E - U P V D , L a b o r a t o i r e d ’ E x c e l l e n c e “ C O R A I L ” , U n i v e r s i t e ́ d e P e r p i g n a n C B E T M , 5 8 r u e P a u l A l d u y , 6 6 8 6 0 , P e r p i g n a n C e d e x , F r a n c e , 3 C o a s t a l a n d F r e s h w a t e r G r o u p , C a w t h r o n I n s t i t u t e , 9 8 H a l i f a x S t r e e t E a s t , 7 0 1 0 , N e l s o n , N e w Z e a l a n d , 4 M a r i n e S c i e n c e a n d T e c h n o l o g y C e n t r e , K l a i p e d a U n i v e r s i t y , H . M a n t o 8 4 , L T - 9 2 2 9 4 , K l a i p e d a , L i t h u a n i a a 1 1 1 1 1 * l a u r a c l u s a @ g m a i l . c o m A b s t r a c t O P E N A C C E S S C i t a t i o n : C l u s a L , A r d u r a A , G o w e r F , M i r a l l e s L , T s a r t s i a n i d o u V , Z a i k o A , e t a l . ( 2 0 1 6 ) A n E a s y P h y l o g e n e t i c a l l y I n f o r m a t i v e M e t h o d t o T r a c e t h e G l o b a l l y I n v a s i v e P o t a m o p y r g u s M u d S n a i l f r o m R i v e r ’ s e D N A . P L o S O N E 1 1 ( 1 0 ) : e 0 1 6 2 8 9 9 . d o i : 1 0 . 1 3 7 1 / j o u r n a l . p o n e . 0 1 6 2 8 9 9 E d i t o r : R i c h a r d C . W i l l s o n , U n i v e r s i t y o f H o u s t o n , U N I T E D S T A T E S R e c e i v e d : M a r c h 2 1 , 2 0 1 6 A c c e p t e d : A u g u s t 3 0 , 2 0 1 6 P u b l i s h e d : O c t o b e r 5 , 2 0 1 6 C o p y r i g h t : 2 0 1 6 C l u s a e t a l . T h i s i s a n o p e n a c c e s s a r t i c l e d i s t r i b u t e d u n d e r t h e t e r m s o f t h e C r e a t i v e C o m m o n s A t t r i b u t i o n L i c e n s e , w h i c h p e r m i t s u n r e s t r i c t e d u s e , d i s t r i b u t i o n , a n d r e p r o d u c t i o n i n a n y m e d i u m , p r o v i d e d t h e o r i g i n a l a u t h o r a n d s o u r c e a r e c r e d i t e d . P o t a m o p y r g u s a n t i p o d a r u m ( N e w Z e a l a n d m u d s n a i l ) i s a p r o s o b r a n c h m o l l u s k n a t i v e t o N e w Z e a l a n d w i t h a w i d e i n v a s i v e d i s t r i b u t i o n r a n g e . I t s n o n - i n d i g e n o u s p o p u l a t i o n s a r e r e p o r t e d f r o m A u s t r a l i a , A s i a , E u r o p e a n d N o r t h A m e r i c a . B e i n g a n e x t r e m e l y t o l e r a n t s p e c i e s , P o t a m o p y r g u s i s c a p a b l e t o s u r v i v e i n a g r e a t r a n g e o f s a l i n i t y a n d t e m p e r a t u r e c o n d i t i o n s , w h i c h e x p l a i n s i t s h i g h i n v a s i v e n e s s a n d s u c c e s s f u l s p r e a d o u t s i d e t h e n a t i v e r a n g e . H e r e w e r e p o r t t h e f i r s t f i n d i n g o f P o t a m o p y r g u s a n t i p o d a r u m i n a b a s i n o f t h e C a n t a b r i a n c o r r i d o r i n N o r t h I b e r i a ( B a y o f B i s c a y , S p a i n ) . T w o h a p l o t y p e s a l r e a d y d e s c r i b e d i n E u r o p e w e r e f o u n d i n d i f f e r e n t s e c t o r s o f R i v e r N o r a ( N a l o n b a s i n ) , s u g g e s t i n g t h e s e c o n d a r y i n t r o d u c t i o n s f r o m e a r l i e r e s t a b l i s h e d i n v a s i v e p o p u l a t i o n s . T o e n h a n c e t h e s u r v e i l l a n c e o f t h e s p e c i e s a n d t r a c k i n g i t s f u r t h e r s p r e a d i n t h e r e g i o n , w e d e v e l o p e d a s p e c i f i c s e t o f p r i m e r s f o r t h e g e n u s P o t a m o p y r g u s t h a t a m p l i f y a f r a g m e n t o f 1 6 S r D N A . T h e s e q u e n c e s o b t a i n e d f r o m P C R o n D N A e x t r a c t e d f r o m t i s s u e a n d w a t e r s a m p l e s ( e n v i r o n m e n t a l D N A , e D N A ) w e r e i d e n t i c a l i n e a c h l o c a t i o n , s u g g e s t i n g c l o n a l r e p r o d u c t i o n o f t h e i n t r o d u c e d i n d i v i d u a l s . M u l t i p l e i n t r o d u c t i o n e v e n t s f r o m d i f f e r e n t s o u r c e p o p u l a t i o n s w e r e i n f e r r e d f r o m o u r s e q u e n c e d a t a . T h e e D N A t o o l d e v e l o p e d h e r e c a n s e r v e f o r t r a c i n g N e w Z e a l a n d m u d s n a i l p o p u l a t i o n s o u t s i d e i t s n a t i v e r a n g e , a n d f o r i n v e n t o r y i n g m u d s n a i l p o p u l a t i o n a s s e m b l a g e s i n t h e n a t i v e s e t t i n g s i f h i g h t h r o u g h p u t s e q u e n c i n g m e t h o d o l o g i e s a r e e m p l o y e d . D a t a A v a i l a b i l i t y S t a t e m e n t : A l l s e q u e n c e s f r o m t h i s w o r k a r e a v a i l a b l e i n t h e G e n b a n k d a t a b a s e ( a c c e s s i o n n u m b e r s K U 9 3 2 9 8 9 - K U 9 3 3 0 1 0 ) . F u n d i n g : T h i s w o r k w a s s u p p o r t e d b y t h e S p a n i s h p r o j e c t M I N E C O - 1 3 - C G L 2 0 1 3 - 4 2 4 1 5 - R a n d t h e A s t u r i a s R e g i o n a l G r a n t G R U P I N - 2 0 1 4 - 0 9 3 . L a u r a C l u s a h o l d s a P C T I G r a n t f r o m t h e A s t u r i a s R e g i o n a l G o v e r n m e n t , r e f e r e n c e d B P 1 4 - 1 4 5 . A l b a A r d u r a h o l d s a r e g i o n a l p o s t d o c t o r a l M a r i e C u r i e g r a n t C O F U N D - C L A R I N . I n t r o d u c t i o n H u m a n - m e d i a t e d t r a n s l o c a t i o n s o f m a r i n e o r g a n i s m s h a v e b e c o m e a w i d e l y a c k n o w l e d g e d g l o b a l e n v i r o n m e n t a l i s s u e n o w a d a y s [ 1 , 2 ] . M a r i t i m e a c t i v i t i e s l i k e m e r c h a n t s h i p p i n g o r y a c h t i n g a i d t h e s p r e a d o f m a n y s p e c i e s o u t o f t h e i r n a t i v e d i s t r i b u t i o n r a n g e , a n d g l o b a l c h a n g e m a y f a c i l i t a t e t h e s u c c e s s o f e x o t i c s p e c i e s i n r e c i p i e n t e c o s y s t e m s u n t i l t h e y b e c o m e P L O S O N E | D O I : 1 0 . 1 3 7 1 / j o u r n a l . p o n e . 0 1 6 2 8 9 9 O c t o b e r 5 , 2 0 1 6 1 / 1 6 A P h y l o g e n e t i c a l l y I n f o r m a t i v e M e t h o d t o T r a c e M u d S n a i l I n v a s i o n i n e D N A f r o m W a t e r S a m p l e s C o m p e t i n g I n t e r e s t s : T h e a u t h o r s h a v e d e c l a r e d t h a t n o c o m p e t i n g i n t e r e s t s e x i s t . i n v a s i v e w i t h a d v e r s e e f f e c t s o n e n v i r
{ "id" : "jmedgenet-2011-100468" , "text" : " G e n o t y p e - p h e n o t y p e c o r r e l a t i o n s O R I G I N A L A R T I C L E C o m p r e h e n s i v e s e q u e n c e a n a l y s i s o f n i n e U s h e r s y n d r o m e g e n e s i n t h e U K N a t i o n a l C o l l a b o r a t i v e U s h e r S t u d y P o l o n a L e Q u e s n e S t a b e j , 1 Z u b i n S a i h a n , 2 , 3 N e l l R a n g e s h , 4 H e a t h e r B S t e e l e - S t a l l a r d , 1 J o h n A m b r o s e , 5 A l i s o n C o f f e y , 5 J e n n y E m m e r s o n , 5 E l e n e H a r a l a m b o u s , 1 Y a s m i n H u g h e s , 1 K a r e n P S t e e l , 5 L i n d a M L u x o n , 4 , 6 A n d r e w R W e b s t e r , 2 , 3 M a r i a B i t n e r - G l i n d z i c z 1 , 6 < A d d i t i o n a l m a t e r i a l s a r e p u b l i s h e d o n l i n e o n l y . T o v i e w t h e s e f i l e s p l e a s e v i s i t t h e j o u r n a l o n l i n e ( h t t p : //jmg.bmj. com/content/49/1.toc). 1 Clinical and Molecular Genetics, Institute of Child Health, UCL, London, UK 2 Institute of Ophthalmology, UCL, London, UK 3 Moorfields Eye Hospital, London, UK 4 Audiovestibualar Medicine, Institute of Child Health, UCL, London, UK 5 Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK 6 UCL Ear Institute, London, UK Correspondence to Dr Maria Bitner-Glindzicz, Clinical and Molecular Genetics Unit, Institute of Child Health, UCL, 30 Guilford Street, London WC1N 1EH, UK; mbitnerg@ich.ucl.ac.uk Received 31 August 2011 Revised 13 October 2011 Accepted 15 October 2011 Published Online First 1 December 2011 ABSTRACT Background Usher syndrome (USH) is an autosomal recessive disorder comprising retinitis pigmentosa, hearing loss and, in some cases, vestibular dysfunction. It is clinically and genetically heterogeneous with three distinctive clinical types (IeIII) and nine Usher genes identified. This study is a comprehensive clinical and genetic analysis of 172 Usher patients and evaluates the contribution of digenic inheritance. Methods The genes MYO7A, USH1C, CDH23, PCDH15, USH1G, USH2A, GPR98, WHRN, CLRN1 and the candidate gene SLC4A7 were sequenced in 172 UK Usher patients, regardless of clinical type. Results No subject had definite mutations (nonsense, frameshift or consensus splice site mutations) in two different USH genes. Novel missense variants were classified UV1-4 (unclassified variant): UV4 is ‘ probably pathogenic’ , based on control frequency <0.23%, identification in trans to a pathogenic/probably pathogenic mutation and segregation with USH in only one family; and UV3 (‘ likely pathogenic’ ) as above, but no information on phase. Overall 79% of identified pathogenic/UV4/UV3 variants were truncating and 21% were missense changes. MYO7A accounted for 53.2%, and USH1C for 14.9% of USH1 families (USH1C: c.496+1G>A being the most common USH1 mutation in the cohort). USH2A was responsible for 79.3% of USH2 families and GPR98 for only 6.6%. No mutations were found in USH1G, WHRN or SLC4A7. Conclusions One or two pathogenic/likely pathogenic variants were identified in 86% of cases. No convincing cases of digenic inheritance were found. It is concluded that digenic inheritance does not make a significant contribution to Usher syndrome; the observation of multiple variants in different genes is likely to reflect polymorphic variation, rather than digenic effects. INTRODUCTION Usher syndrome (USH) is an autosomal recessive disease characterised by the association of sensorineural hearing loss, retinitis pigmentosa (RP) and in some cases by vestibular dysfunction. The disorder is divided into three clinical types: type I (USH1) characterised by profound congenital hearing loss, absent vestibular function and onset of RP usually within the first decade of life; type II (USH2), J Med Genet 2012;49:27e36. doi:10.1136/jmedgenet-2011-100468 characterised by congenital, moderate to severe hearing loss, with normal vestibular function and onset of RP around or after puberty; and type III (USH3), defined by postlingual progressive hearing loss and variable vestibular response together with RP.1 2 In addition there remain patients whose disease does not fit into any of these three subtypes, because of atypical audiovestibular or retinal findings, who are said to have ‘ atypical Usher syndrome’ . Eleven loci and nine genes are associated with USH and cases of digenic inheritance have been described.3e16 For USH1, five associated genes have