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Recent Releases of org.incenp

org.incenp - SSSOM-Java 1.8.1

Changes since version 1.8.0:

  • core: Added support for set-level, propagatable curation_rule and curation_rule_text slots.
  • sssom-cli: When removing mapping_cardinality from the output (--cardinality REMOVE, which is the default behaviour), also removes any cardinality_scope slot.

- Java
Published by gouttegd 7 months ago

org.incenp - SSSOM-Java 1.8.0

Changes since version 1.7.0:

Core library

  • Added support for the new cardinality_scope slot.

Command-line tool

  • New option --input-format to allow overriding the automatic detection of the format of input files.
  • New option --blanket-rule to allow quickly specifying a SSSOM/T rule that should apply to all mappings without having to explicitly use a catch-all filter.
    • For example, use --blanket-rule invert() to invert all mappings.
    • This is a shortcut for --rule "predicate==* -> invert()".
  • New option --cardinality {REMOVE|KEEP|FORCE} to control what to do with mapping cardinality values when producing the output files:
    • REMOVE removes all cardinality values (this is the default behaviour);
    • KEEP leaves any cardinality value in place;
    • FORCE re-computes all cardinality values and overwrites any pre-existing value; this replaces the (now deprecated) option --force-cardinality.

SSSOM/T

  • New function infer_cardinality([scope]) to force the recomputing of cardinality values within a SSSOM/T ruleset.

ROBOT plugin

  • The sssom:inject command can now produce a full SSSOM/OWL export of a mapping set.
  • The default value of the /annots_uris flag in SSSOM/T-OWL is now standard_map.

Deprecation warning: All pre-1.0 features of SSSOM/T-OWL (all features listed here) are going to be removed in the next version. Update your SSSOM/T-OWL rulesets accordingly!

- Java
Published by gouttegd 7 months ago

org.incenp - SSSOM-Java 1.7.0

Changes since version 1.6.0:

Core library

  • Fix incorrect validation of sets containing a mix of records with and without a record_id slot.
  • Add a helper class to facilitate merging two sets.
  • Allow extracting a value from a set using an abstract syntax (soon to be proposed to the SSSOM specification).
  • Support URI-typed extension slots (extensions defined with a type_hint of xsd:anyURI).

SSSOM/T

  • Add missing placeholders for the recently introduced slots mapping_tool_id and record_id.
  • Add a new substitution modifier function (default) to insert a default value if a placeholder would not inject anything (e.g. ${object_label|default('no label')} would inject “no label” if the current mapping does not have a object_label).
  • Add a new filter has_extension to filter mappings depending on the existence of an extension slot.

Command-line tool

  • Add the --no-stdout option to disable writing the result set to standard output.
  • Add the --extract option to extract an arbitrary value from the result set.
    • For example, --extract mapping(2).slot(creator_id, 1) would print the ID of the first creator of the second mapping in the set.
    • See the documentation for more details about the argument to the --extract option.

- Java
Published by gouttegd 8 months ago

org.incenp - SSSOM-Java 1.6.0

Changes since version 1.5.1:

Core library

  • Added support for new slots from the upcoming version 1.1 of the SSSOM specification:
    • record_id,
    • mapping_tool_id,
    • and mapping_set_confidence.
  • In SSSOM 1.1 compliance mode, URI-typed slots are checked for correctness (their values must indeed be a URI).
  • All readers now automatically make additional validity checks by default:
    • presence of a mapping_set_id slot,
    • presence of a license slot,
    • correct use of the record_id slot (if the slot is used at all, then all records must have a unique value).
  • A new experimental feature allows to generate a unique hash for a mapping record.

RDF serialisation

The RDF writers and parsers have been tweaked based on discussions about what the RDF serialisation of SSSOM should look like. Note that those discussions are still ongoing, and the RDF serialisation is still not specified, so it may still change in the future.

The main difference compared with previous versions is that a mapping set is represented by its mapping_set_id, rather than by a blank node. That is, instead of:

ttl [] a sssom:MappingSet ; sssom:mapping_set_id "https://example.org/myset/"^^xsd:anyURI .

this is now:

ttl <https://example.org/myset> a sssom:MappingSet .

(The former representation is still accepted when reading from RDF.)

Likewise, a mapping record is represented using its record_id if present (otherwise, a blank node is still used).

Command-line tool (sssom-cli)

A new --lax option allows to disable the additional validity checks mentioned above.

SSSOM/T

New substitution placeholders

Two new substitution placeholders have been added:

  • %{hash}, which inserts a hash value that uniquely represents the mapping record being processed;
  • and %{serial}, which inserts a number that is automatically incremented whenever a new mapping is processed.

Such placeholders can be used, for example, to automatically generate values for the record_id slot:

subject==* -> assign("record_id", "https://example.org/records/%{hash}");

to generate a record ID of the form https://example.org/records/<UNIQUE_HASH>, or

subject==* -> assign("record_id", "https://example.org/records/%{serial|format(%07d)}");

to generate a record ID of the form https://example.org/records/NNNNNNN.

New filter function

A new filter function, is_duplicate, allows to select mappings for which a mapping-derived value is identical to that of a previously processed mapping.

For example, to filter out all mappings with the same subject_id except the first one:

is_duplicate(%{subject_id}) -> stop();

To filter out all mappings that have the same triple subject_id / predicate_id / object_id, except the first one:

is_duplicate("%{subject_id}%{predicate_id}%{object_id}") -> stop();

Or, using the aforementioned %{hash} substitution, to filter out all mappings that are completely identical, keeping only the first such mapping:

is_duplicate(%{hash}) -> stop();

- Java
Published by gouttegd 9 months ago

org.incenp - SSSOM Java 1.5.1

Changes since version 1.5.0:

  • sssom-cli:
    • New option --assume-version to change the version of the SSSOM specification that a set is assumed to be compliant with, in the absence of an explicit sssom_version slot (default: 1.0, as mandated by the specification).
    • New option --ignore-missing-imports, to silently ignore any failure to load an imported ontology, when using the --update-from-ontology feature.

- Java
Published by gouttegd 10 months ago

org.incenp - SSSOM-Java 1.5.0

Changes since version 1.4.0:

  • Added support for the new sssom_version slot that will be part of the next version (1.1) of the specification.

- Java
Published by gouttegd 10 months ago

org.incenp - SSSOM-Java 1.4.0

Changes since SSSOM-Java 1.3.0:

  • sssom-core:
    • When reading from SSSOM/TSV or SSSOM/JSON files, it is now possible to pre-declare prefixes before reading. Prefix declarations from embedded prefix maps take precedence. This can allow reading sets with incomplete prefix maps.
  • sssom-ext:
    • Fixed a bug in the EPM-based canonicalisation of IRIs.
  • sssom-cli:
    • New option --epm-mode=<PRE|POST|BOTH> to control how to use an Extended Prefix Map (EPM).
    • Some options have been renamed (old names still supported for compatibility):
    • --mangle-iris renamed to --epm;
    • --sssompy-json renamed to --json-sssompy.

- Java
Published by gouttegd 11 months ago

org.incenp - SSSOM-Java 1.3.0

Changes since version 1.2.0:

  • Allow writing mappings without sorting them (--no-sorting option in SSSOM-CLI).
  • Change the type of the see_also slot to URI rather than string.
  • SSSOM/T-OWL:
    • Render URI-typed slots with a proper xsd:anyURI datatype.
    • Add the /annots_uris optional flag to generator functions, to control how metadata slots should be translated into annotation properties.

- Java
Published by gouttegd 11 months ago

org.incenp - SSSOM-Java 1.2.0

Changes since version 1.1.2:

  • Add support for the (upcoming) set-level similarity_measure slot.
  • Add read/write support for the (unofficial) “SSSOM/CSV” format – basically the same format as SSSOM/TSV, but with columns separated by commas rather than by tabs. That format is not part of the SSSOM specification, but is supported by SSSOM-Py and already used in the wild.
  • The SSSOM/TSV reader no longer refuses to parse a TSV file without any set-level metadata block (neither embedded nor external).

- Java
Published by gouttegd about 1 year ago

org.incenp - SSSOM-Java 1.1.2

Changes since version 1.1.1:

  • Fix a recently introduced bug that prevented SSSOM-CLI from opening a SSSOM/TSV with an external metadata block, unless the external metadata file was explicitly specified.
  • SSSOM-CLI now tries using the output filename’s extension to infer the output format, if possible.

- Java
Published by gouttegd about 1 year ago

org.incenp - SSSOM-Java 1.1.1

Changes since version 1.1.0:

  • Add support for propagation and condensation of slots with the RDF/Turtle format.
    • In SSSOM-CLI, condensation is disabled by default when writing to RDF/Turtle; use the --condensation option to enable it.
  • Add support reading non-standard metadata from a RDF/Turtle file.

- Java
Published by gouttegd about 1 year ago

org.incenp - SSSOM-Java 1.1.0

Changes since version 1.0.0:

  • sssom-core:
    • Support the new entity_type value composed entity expression.
    • Support the new predicate_type slot.
    • When reading from a SSSOM/TSV file, strip trailing tabs in the embedded YAML metadata block. This is a workaround to allow reading a file that has been mangled by a non-SSSOM-aware spreadsheet editor.
    • Improved new ISlotVisitor interface.
  • sssom-ext:
    • Support for Extended Prefix Maps (EPMs) moved from the Core library to the Extended Library.
    • Support reading and writing a mapping set to and from the RDF/Turtle format (see below).
  • SSSOM-CLI:
    • Can now read and write files in RDF/Turtle in addition to SSSOM/TSV and SSSOM/JSON.
    • New option -f, --output-format to select the output format (allowed values: tsv, json, ttl). The --json-output option is still supported but is deprecated in favor of --output-format json.
  • SSSOM/Transform:
    • Allow passing an explicit inverse predicate to the invert() function.
    • Allow filtering on the predicate_type slot.
  • SSSOM/T-OWL:
    • Allow using the is_a function on object and data properties, instead of only classes.
    • Allow using the exists function on all type of OWL entities.

About RDF/Turtle support

As the RDF serialisation is not formally specified by the SSSOM standard, RDF/Turtle support has been designed to match the output of SSSOM-Py’s convert -O rdf command. The produced output should not be considered definitive and could change in the future.

Non-standard metadata slots (“extensions”) are currently only supported when writing, not when reading. That is, the RDF/Turtle writer can write a mapping set containing non-standard metadata, but the RDF/Turtle reader will ignore all non-standard metadata when reading a set from a RDF/Turtle file.

Breaking API changes

  • The SlotVisitor and SimpleSlotVisitor interfaces have been replaced by new ISlotVisitor and ISimpleSlotVisitor interfaces with slightly different methods.
  • Some classes have been moved to new packages:
    • the SlotHelper class has been moved to the new org.incenp.obofoundry.sssom.slots package;
    • the ExtendedPrefixMap class has been to the new org.incenp.obofoundry.sssom.util package, in the Extended Library.

- Java
Published by gouttegd about 1 year ago

org.incenp - SSSOM-Java 1.0.0

Changes since version 0.9.0:

  • sssom-core:
    • The core module is now strictly dedicated to the implementation of the SSSOM specification. All additional features (such as SSSOM/Transform) have been moved to a new module called sssom-ext. This is so that library users who just need to read and write mapping sets and perform their own operations on mappings can do so without bringing the whole SSSOM/Transform or OWL-related features that they may not need.
  • SSSOM/Transform:
    • Add the possibility to define filter functions, to filter mappings by executing some custom, application-specific code.
    • Add the possibility to define callback functions, to execute custom code intended to have side-effects on the SSSOM/T engine.
    • Add optional named arguments (“flags”) to function calls.
    • Two features that were previously specific to the SSSOM/T-OWL dialect have now been consolidated and generalised into the base SSSOM/T lamguage:
    • placeholder substitutions in function arguments, e.g. the possibility to write "%{subject_id}" to insert the subject ID of the current mapping;
    • the possibility to define variables that can be dereferenced in a placeholder substitution.
    • Add experimental support for URI Expressions.
  • New functions in SSSOM/T-OWL:
    • exists, to check whether an entity exists in the ontology and is not obsolete;
    • is_a, to check whether an entity is a descendant of another entity;
    • annotate, to add arbitrary annotations on entity.

Breaking change for SSSOM/T-OWL users

Variables dereferenced within a call to create_axiom should no longer be enclosed in angled brackets, as this will prevent them from being successfully recognised by the Manchester syntax parser. To dereference a variable in a call create_axiom, use either the un-bracketed form without angled brackets (%MY_VARIABLE), or the (new in this version) bracketed form with angled brackets (<%{MY_VARIABLE}>).

- Java
Published by gouttegd over 1 year ago

org.incenp - SSSOM-Java 0.9.0

Changes since version 0.8.0:

  • sssom-core:
    • Add support for the special value sssom:NoTermFound.
    • Add support for similarity_score and similarity_measure slots (old slots semantic_similarity_* are still supported when reading, and converted to their renamed variants).
    • Add support for “literal mappings” as defined in the upcoming version 1.0 of the SSSOM specification (“old-style” literal mappings that were defined in the now deprecated “literal profile” of the spec are supported when reading, and automatically converted to their 1.0 equivalent).
    • The parser now accepts date and time values (e.g. 20240809T21:12:30), in addition to pure date values, in the mapping_date slot. The time part is silently discarded.
  • SSSOM/T:
    • It is now possible to select mappings that have no value for a given slot.
    • For free-form text slots, this is done by filtering on the empty string (example: mapping_tool=="" -> ... will apply to mappings with an empty mapping_tool slot).
    • For entity reference slots, this is done by filtering on the special value ~ (example: subject==~ -> ... will apply to mappings with an empty subject_id slot).
  • sssom-cli:
    • Input files can now be specified as positional arguments in addition to (or instead of) -i options. That is, sssom-cli my-input-file.sssom.tsv is equivalent to sssom-cli -i my-input-file.sssom.tsv.

- Java
Published by gouttegd over 1 year ago

org.incenp - SSSOM-Java 0.8.0

Changes since version 0.7.9

  • Added JSON support
    • SSSOM-Core now provides a parser and writer for the JSON serialisation format.
    • As the JSON format is not fully specified yet, three “flavours” of JSON are supported:
    • pure JSON with full-length identifiers,
    • pure JSON with shortened identifiers, with a CURIE map stored in a top-level curie_map slot (not yet officially part of the spec, but should be added soon),
    • “JSON-LD-like” with shortened identifiers, with a CURIE map stored in a top-level @context object (for compatibility with SSSOM-Py; this is not real JSON-LD, it only contains the minimal context needed to make SSSOM-Py happy).
    • All ROBOT commands and the CLI tool can now accept indifferently SSSOM/TSV and JSON files (any flavour).
    • SSSOM-CLI can produce JSON files (any flavour) as output:
    • use --json-output to trigger output in pure JSON with full-length identifiers,
    • add --json-short-iris to trigger output in pure JSON with shortened identifiers,
    • add --json-write-ld-context to trigger output in SSSOM-Py compatibility mode.
  • Other changes:
    • Range constraints of double-typed slots (accepting values between 0.0 and 1.0) are now enforced.

- Java
Published by gouttegd over 1 year ago

org.incenp - SSSOM-Java 0.7.9

Changes since version 0.7.8:

  • The SSSOM/TSV writer now supports writing the metadata block in a separate file.
  • Consequently, the sssom-cli tool gets a new --metadata-output option to write the metadata to a separate file.
  • The --update-from-ontology option accepts new flags to allow for better control of what gets updated:
    • label to update subject_label and/or object_label;
    • source to update subject_source and/or object_source;
    • existence to remove a mapping if the subject and/or object does not exist (or is obsolete);
    • subject to only consider the subject side of mappings;
    • object to only consider the object side of mappings.

- Java
Published by gouttegd over 1 year ago

org.incenp - SSSOM-Java 0.7.8

Changes since version 0.7.7:

  • The SSSOM/TSV writer now writes scalar values in YAML “plain style” whenever possible.
  • Incorrect parsing of some unquoted scalar values in the metadata block has been fixed.
  • Incorrect handling of missing extension values has been fixed.
  • The propagation and condensation of “propagatable slots” is now deactivatable. With sssom-cli, new options --no-propagation and --no-condensation have been added to that effect.

- Java
Published by gouttegd over 1 year ago

org.incenp - SSSOM-Java 0.7.7

Changes since version 0.7.6:

  • SSSOM/TSV writer (SSSOM-Core):
    • Align the format of floating point values with SSSOM-Py.
    • When a propagatable metadata is effectively propagated to individual mappings, remove it from the set-level metadata.
  • xref-extract (SSSOM-Robot):
    • Fill in the subject_source field with the ontology IRI.
    • Accept multiple spaces in the value of the --map-prefix-to-predicate option.
  • SSSOM-CLI:
    • New option --update-from-ontology to check/update a mapping set against a OWL ontology.

- Java
Published by gouttegd almost 2 years ago

org.incenp - SSSOM-Java 0.7.6

Changes since version 0.7.5:

  • sssom-core:
    • Ignore empty lines when reading a SSSOM/TSV file.
  • sssom-cli:
    • Added convenience options --include and --exclude.
    • Write non-standard metadata by default (--write-extra-metadata now defaults to DEFINED rather than NONE).

- Java
Published by gouttegd almost 2 years ago

org.incenp - SSSOM-Java 0.7.5

Changes since version 0.7.4:

  • The support for non-standard metadata has been updated to align with the latest proposition from the SSSOM specification.
  • When generating OWL axioms, they can now be annotated with values from non-standard metadata slots in addition to the standard slots.
  • When writing a set, if the set is actually empty (contains no mappings), a TSV header line is written. This makes the resulting file readable by the SSSOM/TSV parser.
  • Compatibility with the old slot match_term_type has been improved.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.7.4

Changes since version 0.7.3:

  • The SSSOM/TSV writer now correctly escapes strings in the YAML metadata block and in TSV values.
  • Experimental support for reading and writing non-standard metadata.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.7.3

Changes since version 0.7.2:

  • SSSOM-Core library:
  • SSSOM-Robot plugin:
    • New option --use-input-prefix-map to allow using the prefix map from the input set(s) in SSSOM/T rules.
  • SSSOM-CLI tool:
    • New option --split to write the result set in several chunks splitted along the subject and object ID prefixes.
    • New option --mangle-iris to “reconciliate” the IRIs in a mapping set against an extended prefix map.
    • New option --no-metadata-merge to disable merging of multi-valued metadata slots when merging several input sets.
    • New option --output-metadata to set the metadata of the result set from a specific file.
    • New option --prefix-map to set the transform prefix map from the metadata of a specific file.
    • New option --prefix-map-from-input to fill the transform prefix map with the prefixes from the input set(s).
    • New option --output-prefix-map to control which prefix map should be used to write the result set.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.7.2

Changes since version 0.7.1:

  • SSSOM/T:
    • Add a new function assign() to edit mapping slots with fixed values known at compile-time (this replaces the previously introduced edit() function, which is still available for backwards compatibility but is deprecated).
    • Add a new function replace() to edit mapping slots by performing regex-based search-and-replace operations.
  • ROBOT inject command:
    • Add a new option --error-on-unshortenable-iris to force the command to error out if some IRIs cannot be shortened when generating annotation axioms.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.7.1

This is a bugfix release.

The documentation of the SSSOM/T-OWL dialect used by the inject ROBOT command states that all axiom-generating functions accept an optional argument describing how to annotate the generated axioms, but this was not true for the direct() function, which accepted no such argument.

The only change from version 0.7.0 is that the direct() function now accepts the same optional argument as all the other axiom-generating functions. The default behaviour, when the function is called without argument, is still to generate direct axiom annotations for all the mapping metadata except mapping_cardinality.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.7.0

Changes since version 0.6.2:

  • New ROBOT command to rename entities in a OWL ontology, using a mapping set as data source.
  • New SSSOM/T preprocessing function to edit mappings on the fly.

- Java
Published by gouttegd about 2 years ago

org.incenp - SSSOM-Java 0.6.2

Changes since version 0.6.1:

  • Fix erroneous inversion of object_source slot when inverting a mapping.
  • sssom-cli:
    • Provide a self-executable Jar file (for Unix-like systems only).
    • Add the --rule option to specify a single SSSOM/T rule directly from the command line.
  • sssom-inject:
    • Allow to create annotated axioms using the mapping metadata.

Full Changelog: https://github.com/gouttegd/sssom-java/compare/sssom-java-0.6.1...sssom-java-0.6.2

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.6.1

Changes since version 0.6.0:

  • TSV writer:
    • Write out a default license value if no license is explicitly set.
    • Write out an automatically generated ID if no ID is explicitly set.
  • SSSOM/T:
    • Fix filtering on mapping cardinality to ensure it works correctly even when mappings are dropped during the processing.
  • xref-extract:
    • Try to infer mapping ID and license from the source ontology.
    • New options --set-id and --set-license.
  • sssom-inject:
    • Renamed to inject.

Full Changelog: https://github.com/gouttegd/sssom-java/compare/sssom-java-0.6.0...sssom-java-0.6.1

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.6.0

Changes since version 0.5.0:

  • SSSOM/T can now filter on all available slots.
  • Changes to the TSV reader:
    • Silently ignores unknown slots.
    • Recognises and converts slots from older versions of the specification.
    • Propagates slots down to individual mappings.
  • Changes to the TSV writer:
    • Condenses slots up to the level of the mapping set.
  • SSSOM-to-OWL:
    • Excludes mapping_cardinality from OWL serialisation.
    • Use dc/terms rather than dc/elements/1.1 for dispatch table metadata.
  • Addition of sssom-cli, a command-line tool to manipulate mapping sets.

Full Changelog: https://github.com/gouttegd/sssom-java/compare/sssom-java-0.5.0...sssom-java-0.6.0

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.5.0

Changes since version 0.4.3:

  • Fix sssom-inject crash when using --direct option under certain conditions.
  • Fix parsing of multi-valued slots in mappings.
  • Make the output of the TSV writer fully predictable:
    • Sort mapping set metadata by “spec order”.
    • Sort Curie map entries by alphabetical order.
    • Sort mappings using all available slots.
    • Write the effective Curie map only.
  • Add SlotVisitor interface.
  • Add test suite.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.4.3

Changes since version 0.4.2

  • Update model to sssom-0.15.
  • Fix writing of date fields.
  • Fix bogus computation of mapping cardinality.
  • xref-extract:
    • Ignore obsolete classes when extracting cross-references.
    • Allow reusing an existing mapping set (or its metadata).

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.4.2

Changes since version 0.4.1

  • Allow filtering on mapping cardinality (e.g. mapping_cardinality==1:n).
  • Add option --drop-duplicates to xref-extract.
  • Allow to set default ontology ID/version in a dispatch table.
  • Dispatch table filenames are relative to the directory containing the table.

Release artifacts

  • sssom-core-0.4.2.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.4.2.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
  • sssom-robot-standalone-0.4.2.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.4.1

Changes since version 0.4.0

This version brings some helper options to sssom-inject, intended to allow avoiding the use of SSSOM/Transform rules for some simple use cases:

  • --invert to invert the mapping set before generating any bridging axioms.
  • --bridge-iri to specify the ontology IRI of the bridge file created with --bridge-file.
  • --only-subject-in to filter mappings on their subject ID.
  • --only-object-in to filter mappings on their object ID.

In addition, the command now is by default aware of all prefixes that are known to ROBOT when it is called. Use the --no-default-prefixes to revert to the previous behaviour where all prefixes had to be explicitly declared.

Release artifacts

  • sssom-core-0.4.1.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.4.1.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
  • sssom-robot-standalone-0.4.1.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.4.0

Changes since version 0.3.1

  • SSSOM/T-OWL:
    • New preprocessing functions check_subject_existence() and check_object_existence().
    • New function set_var() to declare mapping-dependent variables.
  • New ROBOT command xref-extract to get extract mappings from oboInOwl:hasDbXref annotations in an ontology.
  • New in sssom-inject:
    • Allow loading multiple mapping sets by repeating --sssom option as needed.
    • New option --extract to get a mapping set directly from oboInOwl:hasDbXref annotations in the ontology (may be combined with --sssom).
    • New add-axiom key in dispatch table entries.

Release artifacts

  • sssom-core-0.4.0.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.4.0.jar is a plugin for ROBOT providing the sssom-inject and xref-extract commands, to be used with a version ROBOT that supports plugins (no such version has been released yet);
  • sssom-robot-standalone-0.4.0.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject and xref-extract commands from this project are readily available as built-in commands.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.3.1

This is a bugfix release to fix the missing dependency in the ROBOT plugin artifact in version 0.3.0.

See the 0.3.0 release for the changes since version 0.2.0.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.3.0

Changes since version 0.2.0

  • Project artifacts now split between sssom-core and sssom-robot.
  • Fix parsing of date fields.
  • Support for arbitrary functions in SSSOM/Transform.
  • New interface to specialise the SSSOM/Transform parser.
  • New options for the sssom-inject ROBOT command:
    • --create, to create a new ontology from mappings;
    • --hasdbxref, to create OBO-style cross-references.

Release artifacts

  • sssom-core-0.3.0.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.3.0.jar is a plugin for ROBOT providing the sssom-inject command, to be used with a version ROBOT that supports plugins (no such version has been released yet);
  • sssom-robot-standalone-0.3.0.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject command from this project is readily available as a built-in command.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.2.0

Changes since version 0.1.0

  • Report all undeclared prefixes once parsing is over, instead of erroring out on the first undeclared prefix.
  • Support inversion of mappings.
  • Support filtering on many more fields.
  • New options for the sssom-inject ROBOT command:
    • --dispatch-table, to write generated axioms to different files;
    • --include-rule, to selectively enable only some rules;
    • --exclude-rule, to selectively disable some rules;
    • --direct, to generate direct OWL serialisation of mappings.

Release artifacts

  • sssom-0.2.0.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.2.0.jar additionally includes the dependencies that are not already provided by the standard ROBOT distribution; as such, that file is suitable for use as a ROBOT plugin, if you have a version of ROBOT that supports such plugins;
  • sssom-robot-standalone-0.2.0.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject command from this project is readily available as a built-in command.

- Java
Published by gouttegd over 2 years ago

org.incenp - SSSOM-Java 0.1.0

This is the initial release of the SSSOM Java library and ROBOT command.

  • sssom-0.1.0.jar is the base Java library containing only the code from this project (dependencies are not included);
  • sssom-robot-plugin-0.1.0.jar additionally includes the dependencies that are not already provided by the standard ROBOT distribution; as such, that file is suitable for use as a ROBOT plugin, if you have a version of ROBOT that supports such plugins;
  • sssom-robot-standalone-0.1.0.jar includes a full distribution of ROBOT 1.9.4, where the sssom-inject command from this project is readily available as a built-in command.

- Java
Published by gouttegd over 2 years ago