diff --git a/wiki/BioJava_BioSQL_ORM.md b/wiki/BioJava_BioSQL_ORM.md index ca9839b..cca9dc6 100644 --- a/wiki/BioJava_BioSQL_ORM.md +++ b/wiki/BioJava_BioSQL_ORM.md @@ -11,7 +11,7 @@ to objects in the `org.biojavax` packages. BioJavaX Design =============== -[BioJavaX](http://biojava.org/wikis/BioJava:BioJavaXDocs/) was officially +[BioJavaX](http://biojava.org/wiki/BioJava%3ABioJavaXDocs) was officially released with BioJava1.5. It extends the `org.biojava` API's and was designed to very closely match the BioSQL schema. This made ORM of [BioJava](http://biojava.org) to BioSQL much more straight forward @@ -27,10 +27,10 @@ files formally define where objects are written in the database. Hibernate mappings are currently defined for the following RDBMS's: -- [PostGres](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/pg) -- [Oracle](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/oracle) -- [MySQL](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/mysql) -- [HyperSonic](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/hsqldb) +- [PostGres](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/pg) +- [Oracle](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/oracle) +- [MySQL](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/mysql) +- [HyperSonic](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/hsqldb) - Derby (comming soon) JPA and Annotations diff --git a/wiki/Enhancement_Requests.md b/wiki/Enhancement_Requests.md index a651163..dcd1ba3 100644 --- a/wiki/Enhancement_Requests.md +++ b/wiki/Enhancement_Requests.md @@ -237,7 +237,7 @@ that seems like a bastardization. Suggestions welcome. ### Ability to fully represent contig assembly The ability to fully represent [EMBL format's CO -lines](http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4_14) +lines](http://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt#3_4_14) in a BioSQL record would be desirable. The CO line is essentially a join of segments of other sequences, like this: @@ -282,7 +282,7 @@ would only consist of gap characters, and be virtual). Should there be a better way of doing this? Related to CO lines, [EMBLs AS -lines](http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4_13) +lines](http://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt#3_4_13) store assembly path information. In essence, these could be stored as feature pairs, one feature on the source contig (or read, another bioentry), the other feature on the assembled contig (the entry with the diff --git a/wiki/Main_Page.md b/wiki/Main_Page.md index a49141f..722172d 100644 --- a/wiki/Main_Page.md +++ b/wiki/Main_Page.md @@ -113,10 +113,10 @@ Contacts Project lead is [Hilmar Lapp](http://lappland.io). Questions should be sent to the BioSQL mailing list at [biosql-l@lists.open-bio.org](mailto:biosql-l%40lists%2eopen-bio%2eorg). -You can also [subscribe](http://open-bio.org/mailman/listinfo/biosql-l) +You can also [subscribe](http://mailman.open-bio.org/mailman/listinfo/biosql-l) to the mailing list to keep up to date with discussions and announcements. In addition, the [biosql-guts -list](http://open-bio.org/mailman/listinfo/biosql-guts-l) is for bug +list](http://mailman.open-bio.org/mailman/listinfo/biosql-guts-l) is for bug tracking and commit messages. diff --git a/wiki/PhyloDBSchema.md b/wiki/PhyloDBSchema.md index 39bddbc..8397e80 100644 --- a/wiki/PhyloDBSchema.md +++ b/wiki/PhyloDBSchema.md @@ -82,7 +82,7 @@ part of. "left\_idx and "right\_idx" specify the left and right values of the nested set optimization structure for efficient hierarchical queries. These values needs to be precomputed by a program, see [J. Celko, SQL for -Smarties](http://rs18.rapidshare.com/files/4441805/Trees_and_Hierarchies_in_SQL_for_Smarties.pdf). +Smarties](https://www.worldcat.org/search?q=isbn%3A0128007613). NODE\_PATH ---------- diff --git a/wiki/Releases.md b/wiki/Releases.md index 7a30ab0..1cebcb3 100644 --- a/wiki/Releases.md +++ b/wiki/Releases.md @@ -90,11 +90,11 @@ on any of the below, please email them to biosql-l@lists.open-bio.org. 5. Update Changes file. *Done. --[Hilmar](http://lappland.io) 23:41, 22 February 2008 (EST)* 6. Update documentation in the repository. *Done, for - [Biopython](http://code.open-bio.org/svnweb/index.cgi/biosql/browse/biosql-schema/trunk/doc/biopython) + [Biopython](https://github.com/biosql/biosql/tree/master/doc/biopython) (see - [PDF](http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biopython/python_biosql_basic.pdf)) + [PDF](https://github.com/biosql/biosql/blob/master/doc/biopython/python_biosql_basic.pdf)) and - [BioJava/Oracle](http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/bj_and_bsql_oracle_howto.htm). + [BioJava/Oracle](https://github.com/biosql/biosql/blob/master/doc/bj_and_bsql_oracle_howto.htm). Unfortunately, realized this not before, but only after branching off, so need to merge all changes to the branch. --[Hilmar](http://lappland.io) 12:06, 24 February 2008 (EST)*