InterMine 3.1.0

We've added Strains to the core data model, with relationships with Organism and Sequence Features.

Here's the new XML snippet in core.xml:

    <!-- core.xml -->
    <class name="Strain" extends="BioEntity" is-interface="true">
        <attribute name="annotationVersion" type="java.lang.String"/>
        <attribute name="assemblyVersion" type="java.lang.String"/>
        <collection name="features" referenced-type="SequenceFeature" reverse-reference="strain" />
    </class>

    <class name="SequenceFeature" extends="BioEntity" is-interface="true">
        <!-- snip -->
        <reference name="strain" referenced-type="Strain"  reverse-reference="features" />
    </class>

    <class name="Organism" is-interface="true">
        <!-- snip -->
        <collection name="strains" referenced-type="Strain"/>
    </class>

See our blog post for details on this change.

#1596 - InterMine Core Data model - Annotation, assembly and variety
#1948 - PSI Complexes - remove bad key
#1950 - Remove ecnumbers String from Protein, it's an object now.

InterMine 3.0

We've added SOLR to InterMine!

See Installing Solr and Configuring the keyword search for details for how to install and configure SOLR.

#517 - Improve Lucene search
#562 - Keyword search - speed up initial search
#871 - Replace bobo with Lucene facets
#1632 - Add search facets webservice

InterMine 2.1.1

#1916 - Adds versions to postprocesses

InterMine 2.1.0

InterMine 2.1.0 is a small release that includes some important improvements and bug fixes.

#1583 - Update InterMine code generation to be Python 3 compatible
#1803 - Discontiguous CDS sequences and lengths not set properly
#1844 - FASTA query web service: times out when extensions are used (by @JoelRichardson!)
#1881 - Regions bug: trying to leave extended region field blank results in error message that takes over the page
#1892 - Update publication fails if too many pubmed IDs are sent to the Entrez server (by @nauer)
#1895 - Some SO terms were not updated in 2.0 release

InterMine 2.0

#83 - BioJava - update library
#160 - Create ECO data parser and add descriptions to GO evidence codes
#397 - Spin out the java webservice client from the server code
#412 - Process xrefs correctly in OBO files, e.g. alt_ids
#464 - Remove dependency on tomcat
#482 - Make filter edit / delete icons more clear
#600 - Write up tutorial on how to write a Java source
#611 - Upgrade ant jar
#612 - Maven - try using Gradle instead of Ant for dependency management
#767 - Move sub-projects to their own repo
#831 - Organism config - needs updating
#836 - OrthDB - fail if invalid config
#861 - postprocessing 'do-sources' with many sources fails
#917 - JBrowse - update config
#940 - Need public registry for friendly mines.
#941 - im-ant-tasks JAR can't be created
#971 - PSI Interactions - taxon ID is strain
#983 - Layout.jsp - remove old variable
#1030 - Data sets should have more details - descriptions and pubs
#1093 - Add to list: does not see there other relevant lists when picking items from the table
#1099 - UniprotKB now uses evidence codes from the Evidence Ontology (ECO)
#1109 - Bioseg error messages in postgres on webapp deploy
#1168 - PSI-Complexes -- allow for more data types
#1177 - Genome browser
#1215 - Web services: make template popularity available
#1278 - Checkstyle 6
#1312 - Interactions widget not displaying correctly in live humanMine
#1327 - Query web services should accept JSON queries.
#1343 - Java 8 - Duplicate default methods
#1351 - Postprocess for datasource with multiple entries in the project file
#1358 - Protein molecular weight - change to be a float instead of integer
#1405 - Replace iharder and apache.commons Base64 impls with Base64 in Java 8 SDK
#1450 - org.json jar file is old and lacks some JSON spec methods
#1477 - Update PathQueryHandler deleting code related to the node tag
#1483 - Migrate to gradle
#1510 - Split post-processors out the way data sources are
#1525 - Add SyntenicRegion and SyntenyBlock to core data model
#1531 - Remove legacy code for upgrading
#1602 - FASTA source - make sure biojava.jar is in main/lib
#1604 - Footer broken
#1608 - Java client - requires genomic model
#1620 - Ontology Annotations: Annotate all the things!
#1655 - JSON and XML queries are different
#1656 - Loop constraints are implemented incorrectly in JSON
#1657 - Remove legacy registry code.
#1669 - Add list id to the result of query/tolist service
#1674 - Remove legacy flymine/doc
#1675 - We are using sets and lists interchangably
#1676 - End points have an attribute for queries called "XML". We accept JSON queries so this attribute name is becoming increasingly inaccurate.
#1677 - Delete HintManager
#1684 - Clients - update to use registry
#1689 - Move GO annotation evidence to Ontology annotation
#1694 - UniProt - loading retracted papers
#1697 - Update JSON jar
#1707 - Genomic Intervals as GFF3 - needs strandSpecific parameter
#1719 - NCBI web services - new API rules (3 requests per second)
#1723 - Intermine Registry: please set Access-Control-Allow-Origin
#1734 - Update Chebi JAR
#1738 - Update so.obo to latest version
#1747 - Asking for non-expiring API token should generate one if doesn't exist
#1751 - Registry - add organisation and URL
#1754 - OMIM: not loading a gene-disease relationship
#1759 - BioJava - update JAR
#1761 - HumanMine: External Links broken
#1765 - Update URLGenerator.java to handle HTTPS sites
#1774 - GO: data load now takes 3 hours instead of 10 minutes
#1777 - Region search: update API to include strandSpecific
#1790 - Need old integrate/resources/organism_config.properties functionality
#1792 - Galaxy: export failed - update URL
#1798 - Model change: move HPO annotations to be annotable
#1804 - Panther: bad data
#1812 - Update Postgres and Hikari driver
#1821 - Change taxon ID to be a String
#1831 - GO annotation - new evidence code HDA
#1838 - Update version of Postgres JDBC driver?
#1839 - Galaxy: fix bug that required user to retype the Galaxy URL
#1850 - HumanMine: Some genes don't have Ensembl identifier

InterMine 1.8.5

#1661 - Anonymous session tokens are not authenticating

InterMine 1.8.4

This release is a hodge podge of bug fixes, features, updates to API needed by blue genes and general tidying up.

• The iOS app exposed a race condition in the /service/templates request. This was knocking over some mines!
• Please note all the scripts have been moved to their own repository: intermine/intermine-scripts
• Blue genes is going to use some attributes in web.properties, see the docs for details.
• Special thank you to @vivekkrish and @JoeCarlson for their excellent contributions. (again!)

New features

#1494 - LOOKUP and List upload use BagQueryRunner. Need different "match" behaviour
#1606 - Portal - go to disambiguation page if there are issues
#1607 - Add GTEx data source

Needed by Blue genes

#961 - Need way of referring to lists stably
#1600 - Need web service endpoint to generate permanent API tokens
#1631 - Add defaults web service for each mine
#1652 - Add user ID to web service output

Bug fixes

#1613 - OBO files have terms without names
#1636 - Only look in public schema when counting rows in a table (@JoeCarlson)
#1647 - Enables user login tracking in LOGIN_TRACK_TABLE for OAuth2 flow (@vivekkrish)
#1648 - Templates export in JSON format causes deadlock.

Spring Summer cleaning

#1611 - remove obsolete constraint operators
#1626 - Remove intermine/scripts

InterMine 1.8.3

#1623 Add branding parameters for external apps.

InterMine 1.8.2

#205 - add 4 numbers used to calculate enrichment to web services
#1603 - revert logo changes on footer (temporarily)

InterMine 1.8.1

Update copyright notice.

For the year that's half over. Are we six months late? Maybe we're six months early.