version 1.1

cran · Sep 12, 2022 · 7aded18 · 7aded18
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: bionetdata
 Type: Package
-Title: Biological and chemical data networks
-Version: 1.0.1
-Date: 2014-09-07
-Author: Matteo Re, Giorgio Valentini -- Universita' degli Studi di Milano
-Maintainer: Matteo Re<re@di.unimi.it>
+Title: Biological and Chemical Data Networks
+Version: 1.1
+Date: 2022-09-10
+Author: Giorgio Valentini, Matteo Re -- Universita' degli Studi di Milano
+Maintainer: Giorgio Valentini<valentini@di.unimi.it>
 Description: Data Package that includes several examples of chemical and biological data networks, i.e. data graph structured.
 License: GPL (>= 2)
 LazyLoad: yes
 Depends: R (>= 2.10)
-Packaged: 2014-09-07 09:28:57 UTC; valenti
 NeedsCompilation: no
+Packaged: 2022-09-10 15:43:31 UTC; valenti
 Repository: CRAN
-Date/Publication: 2014-09-07 13:10:15
+Date/Publication: 2022-09-12 08:12:59 UTC
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-098a33b1418405aab3796204058bad87 *DESCRIPTION
+f721485085b34b14e562f32f2bb45948 *DESCRIPTION
 9fdfeb11f7ddba6f3aab9aaa6b1ac5dd *NAMESPACE
 f701d5381aebaaec5e3b35a507e63c71 *data/CGM.Cat.rda
 86231782f700e3ac1c331af1a2e14fbb *data/DD.chem.data.rda
@@ -9,13 +9,13 @@ dfa44f72c91c29769b775e334eb3ae5f *data/Yeast.Biogrid.data.rda
 55f35a96128e8c58836d43c13eff2717 *data/Yeast.STRING.FunCat.rda
 4fbde98ef52dde4ba0121a0d4e323b3d *data/Yeast.STRING.data.rda
 d1e4fd8bcd4fcabcdc6cef5ebf589cc3 *data/datalist
-d2ce6b6846cb6983cd2913319c9827b7 *inst/doc/bionetdata.pdf
-497a87a92681afe17d106c1620472e3e *man/CGM.Cat.Rd
-aff8e4bece30fa9c7068736e6ed4ac45 *man/DD.chem.data.Rd
-ecb8bd5bfe6f7a90de784710896bd7fd *man/DrugBank.Cat.Rd
+d60c46042dedf79b7cc52b179c2b16f1 *inst/doc/bionetdata.pdf
+5846dde2a7c2ebb202c64472afb2a729 *man/CGM.Cat.Rd
+11c3ab30442d72638c08ca5fb720396e *man/DD.chem.data.Rd
+b119b9d39741a13fa0e4455d6b8221e6 *man/DrugBank.Cat.Rd
 7e6527e91e28fcb133d5c94ea338ddea *man/FIN.data.Rd
-5ca86e9241fc68eb5d63b7223ae5a255 *man/Yeast.Biogrid.FunCat.Rd
-81f4f446a86dfbc8539f432847cc8573 *man/Yeast.Biogrid.data.Rd
-95bdd228780c4cab0b4add54df660a81 *man/Yeast.STRING.FunCat.Rd
-9f3add07d8ad3e54a1f2dfa4ef02f63b *man/Yeast.STRING.data.Rd
-606f21636b07200eda5295a054a6dc47 *man/bionetdata-package.Rd
+7afda3ae55b85ba69993e0cfed5e7fed *man/Yeast.Biogrid.FunCat.Rd
+c6722ae47558066c2c54d6a3e05d84f2 *man/Yeast.Biogrid.data.Rd
+7ea8142c511e7b7f6025d4a534257b75 *man/Yeast.STRING.FunCat.Rd
+98651cf52fd2264f661e829c8f3fa88e *man/Yeast.STRING.data.Rd
+f2b05fbf86144732bc59d71d1358a014 *man/bionetdata-package.Rd
diff --git a/inst/doc/bionetdata.pdf b/inst/doc/bionetdata.pdf
diff --git a/man/CGM.Cat.Rd b/man/CGM.Cat.Rd
@@ -30,7 +30,7 @@ A 2033 x 10 named matrix where rows refer to human gene symbols, columns to 10 C
 \source{
 Original annotations (c4.cm.v3.0.symbols.gmt) are available at: 
 
-\url{http://www.broadinstitute.org/gsea/msigdb} 
+\url{http://software.broadinstitute.org/gsea/msigdb} 
 }
 \references{
 Segal E., Friedman N., Koller D. and Regev A., A module map showing conditional activity of

diff --git a/man/DD.chem.data.Rd b/man/DD.chem.data.Rd
@@ -15,9 +15,8 @@ Chemical structure similarities between 1253 FDA approved drugs obtained from Dr
 This matrix contains the Tanimoto chemical structure similarity scores between 1253 DrugBank drugs. Canonical Simplified molecular-input line-entry specifications (SMILES) of the drugs were extracted from the DrugBank Drugcards. The SMILES were then converted into molecular extended fingerprints (1024 bits) using the rcdk package. The set of fingerprints was finally converted into a Tanimoto similarity  matrix using the fp.sim.matrix rcdk function. All the real values contained in this matrix represent the chemical structure similarity between each possible pair of drugs and are comprised between 0 (completely different chimical structures) and 1 (identical chemical structures).
 }
 \source{
-The SMILES representations of the drugs were extracted by the Smiles_String_canonical fields of the DrugCards contained in the file drugbank.txt available at:
-
-\url{http://www.drugbank.ca/system/downloads/current/drugbank.txt.zip} 
+The SMILES representations of the drugs can be obtained from:
+\url{https://go.drugbank.com/releases/latest} 
 }
 \references{
 Wishart, D., Knox, C., Guo, A., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z.,

diff --git a/man/DrugBank.Cat.Rd b/man/DrugBank.Cat.Rd
@@ -15,9 +15,8 @@ A 1253 x 45 named binary matrix where rows refer to DrugBank drugs, columns to 4
 The drug categories were extracted by parsing the Drug_Category field of the DrugBank 3.0 DrugCards of the 1253 FDA approved drugs contained in the \code{\link{DD.chem.data}} matrix. The DrugBank Drug categories are produced by manual curators. On the contrary of other drugs functional annotation schemes these drugs categories are not restricted to specific deseases. Indeed it is possible to find in this functional annotation scheme categories associated to drugs involved in the treatment of specific deseases (i.e. 'AntiParkinsons_Agents') or to the treatment of symptoms (i.e. 'Anticonvulsants') associated to many deseases. This functional labelling scheme contains also categories based on the Mode of Action (MOA) of the drugs as in the case of the 'Adrenergic_Uptake_Inhibitors' category.   
 }
 \source{
-The drug categories were extracted by parsing the Drug_Category field of the DrugCards contained in the file drugbank.txt available at: 
-
-\url{http://www.drugbank.ca/system/downloads/current/drugbank.txt.zip}
+The drug categories can be obtained from:
+\url{https://go.drugbank.com/releases/latest} 
 }
 \references{
 Knox, C., Law, V., Jewison, T., Liu, P., Ly, S., Frolkis, A., Pon, A., Banco, K., Mak, C.,

diff --git a/man/Yeast.Biogrid.FunCat.Rd b/man/Yeast.Biogrid.FunCat.Rd
@@ -14,10 +14,6 @@ data, available from the MIPS web site.
 A named matrix where rows refer to yeast genes, columns to FunCat classes.
 Names of yeast genes are systematic names. Names of columns correspond to FunCat IDs.
 }
-
-\source{
-\url{http://mips.gsf.de/projects/funcat}
-}
 \references{
 Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, I., Guldener, U., Mannhaupt, G., Munsterkotter, M., and Mewes, H. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research, 32(18), 5539-5545.
 }

diff --git a/man/Yeast.Biogrid.data.Rd b/man/Yeast.Biogrid.data.Rd
@@ -18,7 +18,7 @@ Names correspond to systematic names of yeast genes.
 }
 
 \source{
-BioGRID data base: \url{http://thebiogrid.org}
+BioGRID data base: \url{https://thebiogrid.org}
 
 }
 \references{

diff --git a/man/Yeast.STRING.FunCat.Rd b/man/Yeast.STRING.FunCat.Rd
@@ -14,9 +14,6 @@ data, available from the MIPS web site.
 A named matrix where rows refer to yeat genes, columns to FunCat classes.
 Names of yeast genes are systematic names. Names of columns correspond to FunCat IDs.
 }
-\source{
-\url{http://mips.gsf.de/projects/funcat}
-}
 \references{
 Ruepp, A., Zollner, A., Maier, D., Albermann, K., Hani, J., Mokrejs, M., Tetko, I., Guldener, U., Mannhaupt, G., Munsterkotter, M., and Mewes, H. (2004). The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Research, 32(18), 5539-5545.
 }

diff --git a/man/Yeast.STRING.data.Rd b/man/Yeast.STRING.data.Rd
@@ -14,7 +14,7 @@ Binary protein-protein interactions from the STRING data base (von Mering et al.
 }
 
 \source{
-\url{http://string-db.org}
+\url{https://string-db.org}
 }
 \references{
 von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S., Fields, S., and Bork, P. (2002). Comparative assessment of

diff --git a/man/bionetdata-package.Rd b/man/bionetdata-package.Rd
@@ -12,8 +12,8 @@ Data Package that includes several examples of chemical and biological data netw
 \tabular{ll}{
 Package: \tab bionetdata\cr
 Type: \tab Package\cr
-Version: \tab 1.0.1\cr
-Date: \tab 2014-09-07\cr
+Version: \tab 1.1\cr
+Date: \tab 2022-09-10\cr
 License: \tab GPL (>= 2) \cr
 LazyLoad: \tab yes\cr
 }
@@ -26,10 +26,10 @@ DI, Dipartimento di Scienze dell'Informazione
 
 Universita' degli Studi di Milano
 
-\email{\{valentini,re\}@di.unimi.it}
+\email{\{valentini\}@di.unimi.it}
 
 Maintainer: 
-\emph{Matteo Re} 
+\emph{Giorgio Valentini} 
 }