Class information for:
Level 1: CELLML//SBML//AUCKLAND BIOENGN

Basic class information
Class id #P Avg. number of
references		 Database coverage
of references
15220 725 36.3 69%


Bar chart of Publication_year

Last years might be incomplete

Hierarchy of classes
The table includes all classes above and classes immediately below the current class.


Cluster id Level Cluster label #P
0 4 BIOCHEMISTRY & MOLECULAR BIOLOGY//CELL BIOLOGY//ONCOLOGY 4064930
90 3       MATHEMATICAL & COMPUTATIONAL BIOLOGY//BIOINFORMATICS//BMC BIOINFORMATICS 77178
548 2             BMC SYSTEMS BIOLOGY//MATHEMATICAL & COMPUTATIONAL BIOLOGY//BOOLEAN NETWORKS 14655
15220 1                   CELLML//SBML//AUCKLAND BIOENGN 725

Terms with highest relevance score


rank Term termType Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 CELLML authKW 507142 2% 71% 17
2 SBML authKW 440169 2% 58% 18
3 AUCKLAND BIOENGN address 195883 7% 9% 49
4 BIOINFORMAT TUEBINGEN ZBIT address 183765 2% 36% 12
5 BIOPAX authKW 175483 1% 83% 5
6 SBGN authKW 134771 1% 80% 4
7 SCI DATABASES VISUALIZAT GRP address 134771 1% 80% 4
8 BIOMIMET MAT ENGN BIOL TISSUES address 126349 0% 100% 3
9 FIELDML authKW 126349 0% 100% 3
10 PHYSIOME PROJECT authKW 116624 1% 46% 6

Web of Science journal categories


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 Mathematical & Computational Biology 42435 44% 0% 321
2 Biochemical Research Methods 7900 35% 0% 253
3 Biotechnology & Applied Microbiology 3809 31% 0% 226
4 Computer Science, Theory & Methods 298 6% 0% 45
5 Computer Science, Interdisciplinary Applications 177 5% 0% 35
6 Biochemistry & Molecular Biology 116 15% 0% 108
7 Computer Science, Artificial Intelligence 113 4% 0% 28
8 Biology 108 4% 0% 30
9 Multidisciplinary Sciences 97 2% 0% 16
10 Engineering, Biomedical 96 3% 0% 25

Address terms


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 AUCKLAND BIOENGN 195883 7% 9% 49
2 BIOINFORMAT TUEBINGEN ZBIT 183765 2% 36% 12
3 SCI DATABASES VISUALIZAT GRP 134771 1% 80% 4
4 BIOMIMET MAT ENGN BIOL TISSUES 126349 0% 100% 3
5 BIOINFORMAT BIGCAT 87846 2% 19% 11
6 INTEGRAT GENET CIGENE IMT 84233 0% 100% 2
7 INTELLIGENT INFORMAT INFRASTRUCT 84233 0% 100% 2
8 GRP CLIN GENOM NETWORKS 63172 0% 50% 3
9 FISIOCOMP 56154 0% 67% 2
10 INTEGRATED OPEN SYST UNIT 56154 0% 67% 2

Journals


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class
1 BIOINFORMATICS 71113 18% 1% 134
2 BMC SYSTEMS BIOLOGY 68281 7% 3% 51
3 BMC BIOINFORMATICS 13429 7% 1% 49
4 IET SYSTEMS BIOLOGY 10258 1% 3% 9
5 PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY 8104 2% 1% 15
6 JOURNAL OF BIOMEDICAL SEMANTICS 6254 1% 2% 6
7 BRIEFINGS IN BIOINFORMATICS 4891 1% 1% 9
8 WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 3409 1% 2% 5
9 MOLECULAR SYSTEMS BIOLOGY 2716 1% 1% 7
10 DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2317 1% 1% 6

Author Key Words


Rank Term Chi square Shr. of publ. in
class containing
term		 Class's shr. of
term's tot. occurrences		 #P with
term in
class		 LCSH search Wikipedia search
1 CELLML 507142 2% 71% 17 Search CELLML Search CELLML
2 SBML 440169 2% 58% 18 Search SBML Search SBML
3 BIOPAX 175483 1% 83% 5 Search BIOPAX Search BIOPAX
4 SBGN 134771 1% 80% 4 Search SBGN Search SBGN
5 FIELDML 126349 0% 100% 3 Search FIELDML Search FIELDML
6 PHYSIOME PROJECT 116624 1% 46% 6 Search PHYSIOME+PROJECT Search PHYSIOME+PROJECT
7 VIRTUAL PHYSIOLOGICAL HUMAN 112300 1% 33% 8 Search VIRTUAL+PHYSIOLOGICAL+HUMAN Search VIRTUAL+PHYSIOLOGICAL+HUMAN
8 PHYSIOME 110818 1% 26% 10 Search PHYSIOME Search PHYSIOME
9 RULE BASED MODELING 89716 1% 30% 7 Search RULE+BASED+MODELING Search RULE+BASED+MODELING
10 BIOCHEMICAL SIMULATIONS 84233 0% 100% 2 Search BIOCHEMICAL+SIMULATIONS Search BIOCHEMICAL+SIMULATIONS

Core articles
The table includes core articles in the class. The following variables is taken into account for the relevance score of an article in a cluster c:
(1) Number of references referring to publications in the class.
(2) Share of total number of active references referring to publications in the class.
(3) Age of the article. New articles get higher score than old articles.
(4) Citation rate, normalized to year.


Rank Reference # ref.
in cl.		 Shr. of ref. in
cl.		 Citations
1 WALTEMATH, D , BERGMANN, FT , CHAOUIYA, C , CZAUDERNA, T , GLEESON, P , GOBLE, C , GOLEBIEWSKI, M , HUCKA, M , JUTY, N , KREBS, O , ET AL (2014) MEETING REPORT FROM THE FOURTH MEETING OF THE COMPUTATIONAL MODELING IN BIOLOGY NETWORK (COMBINE).STANDARDS IN GENOMIC SCIENCES. VOL. 9. ISSUE 3. P. - 30 64% 0
2 CHYLEK, LA , HARRIS, LA , FAEDER, JR , HLAVACEK, WS , (2015) MODELING FOR (PHYSICAL) BIOLOGISTS: AN INTRODUCTION TO THE RULE-BASED APPROACH.PHYSICAL BIOLOGY. VOL. 12. ISSUE 4. P. - 43 39% 3
3 COSKUN, SA , CICEK, AE , LAI, N , DASH, RK , OZSOYOGLU, ZM , OZSOYOGLU, G , (2013) AN ONLINE MODEL COMPOSITION TOOL FOR SYSTEM BIOLOGY MODELS.BMC SYSTEMS BIOLOGY. VOL. 7. ISSUE . P. - 17 89% 2
4 LI, C , DONIZELLI, M , RODRIGUEZ, N , DHARURI, H , ENDLER, L , CHELLIAH, V , LI, L , HE, EU , HENRY, A , STEFAN, MI , ET AL (2010) BIOMODELS DATABASE: AN ENHANCED, CURATED AND ANNOTATED RESOURCE FOR PUBLISHED QUANTITATIVE KINETIC MODELS.BMC SYSTEMS BIOLOGY. VOL. 4. ISSUE . P. - 16 67% 207
5 NICKERSON, D , ATALAG, K , DE BONO, B , GEIGER, J , GOBLE, C , HOLLMANN, S , LONIEN, J , MULLER, W , REGIERER, B , STANFORD, NJ , ET AL (2016) THE HUMAN PHYSIOME: HOW STANDARDS, SOFTWARE AND INNOVATIVE SERVICE INFRASTRUCTURES ARE PROVIDING THE BUILDING BLOCKS TO MAKE IT ACHIEVABLE.INTERFACE FOCUS. VOL. 6. ISSUE 2. P. - 24 51% 2
6 CHELLIAH, V , JUTY, N , AJMERA, I , ALI, R , DUMOUSSEAU, M , GLONT, M , HUCKA, M , JALOWICKI, G , KEATING, S , KNIGHT-SCHRIJVER, V , ET AL (2015) BIOMODELS: TEN-YEAR ANNIVERSARY.NUCLEIC ACIDS RESEARCH. VOL. 43. ISSUE D1. P. D542 -D548 15 65% 30
7 VAN IERSEL, MP , VILLEGER, AC , CZAUDERNA, T , BOYD, SE , BERGMANN, FT , LUNA, A , DEMIR, E , SOROKIN, A , DOGRUSOZ, U , MATSUOKA, Y , ET AL (2012) SOFTWARE SUPPORT FOR SBGN MAPS: SBGN-ML AND LIBSBGN.BIOINFORMATICS. VOL. 28. ISSUE 15. P. 2016-2021 14 100% 12
8 MISIRLI, G , CAVALIERE, M , WAITES, W , POCOCK, M , MADSEN, C , GILFELLON, O , HONORATO-ZIMMER, R , ZULIANI, P , DANOS, V , WIPAT, A , (2016) ANNOTATION OF RULE-BASED MODELS WITH FORMAL SEMANTICS TO ENABLE CREATION, ANALYSIS, REUSE AND VISUALIZATION.BIOINFORMATICS. VOL. 32. ISSUE 6. P. 908 -917 20 63% 1
9 KOLCZYK, K , CONRADI, C , (2016) CHALLENGES IN HORIZONTAL MODEL INTEGRATION.BMC SYSTEMS BIOLOGY. VOL. 10. ISSUE . P. - 18 75% 0
10 WALTEMATH, D , WOLKENHAUER, O , (2016) HOW MODELING STANDARDS, SOFTWARE, AND INITIATIVES SUPPORT REPRODUCIBILITY IN SYSTEMS BIOLOGY AND SYSTEMS MEDICINE.IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING. VOL. 63. ISSUE 10. P. 1999 -2006 22 55% 1

Classes with closest relation at Level 1


Rank Class id link
1 2029 FLUX BALANCE ANALYSIS//METABOLIC NETWORK//CONSTRAINT BASED MODELING
2 35517 COMPLEX AUTOMATA//DISTRIBUTED MULTISCALE COMPUTING//HPC INFRASTRUCTURE
3 8965 CHEMICAL REACTION NETWORKS//MASS ACTION KINETICS//ULTRASENSITIVITY
4 25430 NEURAL SIMULATOR//FRONTIERS IN NEUROINFORMATICS//ADV SIMULATJULICH AACHEN ALLIANCE
5 12004 STRUCTURAL IDENTIFIABILITY//IDENTIFIABILITY//MODEL DISCRIMINATION
6 5632 BOOLEAN NETWORKS//SEMI TENSOR PRODUCT//BOOLEAN CONTROL NETWORK
7 681 PROTEIN INTERACTION NETWORK//PROTEIN PROTEIN INTERACTION NETWORK//ESSENTIAL PROTEINS
8 18864 DATABASE LIFE SCI//DDBJ//EMTRAIN
9 8123 METABOLIC CONTROL ANALYSIS//BIOCHEMICAL SYSTEMS THEORY//S SYSTEM
10 1585 CHEMICAL MASTER EQUATION//STOCHASTIC GENE EXPRESSION//TAU LEAPING

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