CutAdapt

https://cutadapt.readthedocs.io/en/stable/

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

MIT License (MIT)

http://obo-dashboard-test.ontodev.com/swo/dashboard.html

"Scope" currently fails as we are missing a section in our description of SWO on the OBO foundry site.
The Scope test can pass by adding text as outlined http://obofoundry.org/principles/checks/fp_005 and therefore should be straightforward to fix.

mzCloud

https://www.mzcloud.org/

mzCloud is a state of the art online mass spectral database that assists analysts in identifying compounds in areas such as life sciences, metabolomics, pharmaceutical research, toxicology, forensic investigations, environmental analysis, food control and various industrial applications.

Online access to the database is free of charge and no registration is required.

In some past release, someone created "sequence feature format" with the following odd IRI: http://urigen_local_uri/963a1b3b-49f2-4ef9-8f37-5e9cd5403b2a/http://www.ebi.ac.uk/swo/data/SWO_3000069

This should be rebuilt as http://www.ebi.ac.uk/swo/data/SWO_3000069

SWATH Software

https://sciex.com/technology/swath-acquisition

SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology.

Proprietary commercial software licence

http://obo-dashboard-test.ontodev.com/swo/dashboard.html

The "Plurality of users" check fails because the SWO page on the obo foundry is missing tracker and usages, details of which can be found at http://obofoundry.org/principles/checks/fp_009

We really should have automated the build procedure properly, and this ticket covers the conversion to a ROBOT Makefile.

Possibly a stupid question, but why can't I see the SWO updates on the OLS site? A lot of my tooling relies on the OLS platform rather than the ontobee platform (JSON calls, that sort of thing). Not really an issue, just curious about the difference. Many thanks!

Graphpad Prism

https://www.graphpad.com/scientific-software/prism/

GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers.

Commercial software with 30 day trial period

Hey! In our great OBO wide effort to fix our PURLs, I noticed the following wrong ones being used in SWO:

http://purl.obofoundry.org/obo/IAO_0000136

should be:
http://purl.obolibrary.org/obo/IAO_0000136

Seurat

https://satijalab.org/seurat/

Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.

GNU Public License (GPL 3.0)

Using Protege version 5.5.0, I can successfully open the file swo_merged.owl from the latest release (SWO Release 1.6).

However, the following error is thrown by Protege when trying to open either:

• https://github.com/allysonlister/swo/blob/master/release/1.6/swo_merged.owl
• https://github.com/allysonlister/swo/blob/master/release/swo.owl

Error: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=8:column=17] Expecting rdf:RDF element.

Stack Trace:

org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=8:column=17] Expecting rdf:RDF element.


Full Stack Trace
-----------------------------------------------------------------------------------------

org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFXMLParserException: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=8:column=17] Expecting rdf:RDF element.
	at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1262)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1215)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1172)
	at org.protege.editor.owl.model.io.OntologyLoader.loadOntologyInternal(OntologyLoader.java:104)
	at org.protege.editor.owl.model.io.OntologyLoader.lambda$loadOntologyInOtherThread$0(OntologyLoader.java:62)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=8:column=17] Expecting rdf:RDF element.
	at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.verify(RDFParser.java:451)
	at org.semanticweb.owlapi.rdf.rdfxml.parser.StartRDF.startElement(StartRDF.java:187)
	at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:509)
	at com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startElement(XMLDTDValidator.java:745)
	at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
	at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl$NSContentDriver.scanRootElementHook(XMLNSDocumentScannerImpl.java:613)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:3132)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:852)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:602)
	at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:112)
	at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:505)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:841)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:770)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:643)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:327)
	at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:145)
	at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:73)
	... 10 more

SAMtools

https://github.com/samtools/samtools

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

The MIT/Expat License

Please could @drmarkreuter provide:

1. homepage
2. definition (i.e. purpose)
3. licence info

Apologies for a lack of official term suggestion guidelines - we're volunteer run, and have to budget our time!

Split from #10.

Feel free to add any others to the issue tracker. Thanks!

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

http://obo-dashboard-test.ontodev.com/swo/dashboard.html

The "Maintenance" test fails because the version iri does not have valid date information. Conformance should be straightforward, and details are available at http://obofoundry.org/principles/checks/fp_016

Chromeleon

https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7

Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments.

Proprietary commercial software licence

http://obo-dashboard-test.ontodev.com/swo/dashboard.html

"Versioning" test currently issues a warning about the version being in the wrong format. Should be simple to update to allow the test to pass.

Details of OBO conformance at http://obofoundry.org/principles/fp-004-versioning.html

Some still have outdated IRIs.

RNA-SeQC

https://github.com/broadinstitute/rnaseqc

RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.

BSD 3-clause license

ProteomicsTools

https://github.com/shengqh/RCPA.Tools/wiki

ProteomicsTools software suite contains a bunch of tools used in proteomics research, from identification result parsing to quantification, modification, et. al.

GNU General Public License v3.0

Check that OntoDM terms are up to date, as they are not available in Ontobee.

https://www.osadl.org/Open-Source-License-Checklists.oss-compliance-lists.0.html

This project is launched with the goal to create generally accepted checklists of the obligations of commonly used Open Source software that are accepted by distributors and copyright holders and trusted by all members of the distribution chain.

This might be useful for SWO and should be investigated a bit more as we have time.

Before the next release, resolve messages produced by ROBOT's report feature.

At some point in the past, "matlab software" (http://www.ebi.ac.uk/swo/Class_6) was created with an odd IRI. A new IRI needs generating to have its structure match all other SWO iris.

HTSeq

https://htseq.readthedocs.io/en/release_0.11.1/

HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.

GNU General Public License, version 3

RSeQC

http://rseqc.sourceforge.net/

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.

GNU General Public License (GPLv3)

AnalyzerPro

https://www.spectralworks.com/products/analyzerpro/

AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform

Proprietary commercial software licence

Salmon

https://combine-lab.github.io/salmon/

Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.

GNU GENERAL PUBLIC LICENSE Version 3

I am toying with the idea (and this will be reflected in some commits) of merging the following files back into a single file for ease of curation. We don't really need the division of labor available to us with all of these files, and it would be simpler. The only issue is the auto-generation of IDs. Would it cause any problems in this respect, or might it be OK to have simpler IDs generated from this release onwards as well?

swo_algorithms.owl  
swo_data.owl       
swo_licenses.owl  
swo_objectives.owl     
swo_versions.owl
swo_core.owl        
swo_interface.owl  
swo_maturity.owl  
swo_organizations.owl

http://obo-dashboard-test.ontodev.com/swo/dashboard.html

"Open" test currently fails due to issue with how the dcterms:license is used. Should be simple to update to allow the test to pass. Details at OBOFoundry/OBOFoundry.github.io#1019 (comment)

Details of OBO conformance at http://obofoundry.org/principles/fp-001-open.html

note, this issue is also been posted to IAO Discussion Group at:
https://groups.google.com/forum/#!topic/information-ontology/S07ghF9lGY0

We've been using SWO with great success now for a month. I have one major issue / question:

SWO defines the class "software" (http://www.ebi.ac.uk/swo/SWO_0000001) as a subclass of IAO:information content entity (http://purl.obolibrary.org/obo/IAO_0000030)
URI = http://www.ebi.ac.uk/swo/SWO_0000001
def = Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations.

This class seems redundant with IAO:Software (http://purl.obolibrary.org/obo/IAO_0000010)
class hierarchy = information content entity / directive information entity / plan specification / Software
URI = http://purl.obolibrary.org/obo/IAO_0000010
def = Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.

Should SWO:Software be deleted and it's subclasses moved under IAO:Software to maximize ontology reuse, maintain clean separation between upper / middle / domain ontologies, and to minimize confusion and redundancy?

There are a number of Bioconductor packages that are highly similar. Not only should we revisit these, but we should also improve the modelling of these packages within SWO.

Examples:

http://www.ebi.ac.uk/swo/SWO_0000285
http://www.ebi.ac.uk/swo/SWO_1100044
http://www.ebi.ac.uk/swo/SWO_0000546
http://www.ebi.ac.uk/swo/SWO_0000547
http://www.ebi.ac.uk/swo/SWO_0000494
http://www.ebi.ac.uk/swo/SWO_0000495

Hi,
I have swo as an import. I am using OBO Robot to merge the imports into one ontology file (import closure). However, I am getting an error relating to unable to import http://www.ebi.ac.uk/swo/swo-external.owl. ROBOT gives this as hint for the issue:

Cause: https://www.ebi.ac.uk/ols/ontologies/swo/terms?iri=http://www.ebi.ac.uk/swo/swo-external.owl

It would be nice to have a property that is appropriate for connecting a software like HTSeq (SWO:1100140) to the programming language in which it's implemented like Python (SWO:0000118). This would be useful for the Data Science Ontology for better aligning with OBO as well. CC @epatters

I would label this relation implemented in programming language and it would have the following properties:

1. Range: software (SWO:0000001)
2. Domain: programming language (IAO:0000025)

http://www.ebi.ac.uk/swo/software_before_Microsoft_2007 is not an ID that conforms to the SWO naming scheme. This needs a new IRI with a SWO_ id created.

Class 1:
IRI: http://www.ebi.ac.uk/swo/objective/SWO_4000007
label: "software development"
parent class label: "information processing"

Class 2:
IRI: http://www.ebi.ac.uk/swo/organization/SWO_9000056
label: "software development process"
parent class label: "process"

Class 2 has a definition, so I'm assuming it's the one you intend folks to use, but I'm holding off until one of them is deprecated.

StavroX

http://www.stavrox.com/

StavroX software identifies cross linked peptides.

Freeware Software License (http://www.stavrox.com/license.htm)

Hi Allyson - hope you are well, long time no see!

One of our pharma customers is using SWO and spotted a dupe id: SWO_0000075

In OLS they have slightly different URIs:

http://www.ebi.ac.uk/efo/swo/SWO_0000075
http://www.ebi.ac.uk/swo/SWO_0000075

(the http://www.ebi.ac.uk/efo/swo/ URIs don't resolve anywhere)

thanks

Jane

FastQC

https://github.com/s-andrews/FastQC

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.

GNU GENERAL PUBLIC LICENSE Version 2

As a more general point for discussion, we should determine how best to develop formats in SWO when we may be able to MIREOT them as necessary from other sources (e.g. https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_1915&viewMode=All&siblings=false) to focus more on the software aspects. If @jamesmalone or Helen fancies weighing in on this, please do.

The following issues need resolving:

There is currently a bug in SWO which incorrectly associates BFO 'process' (BFO_0000015) with the wrong URI (BFO_0000007). A new version of BFO should sort this.

The human readable definition (obo:IAO_0000115) for SWO_9000061 currently reads:
Development status is an information content entity which indicates the maturity of a sofrware entity within the context of the software life cycle.

The word "sofrware" is a typo and should be corrected to "software"

PEAKS DB

http://www.bioinfor.com/peaksdb/

Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions.

Proprietary commercial software licence

EDAM class 'differentical gene expression analysis' is listed within EDAM with
a URI of http://edamontology.org/operation_3223, but is imported into SWO as http://edamontology.org/operation_3742. Need to investigate if this is due to an old import, and then fix it.

Please could @drmarkreuter provide:

1. homepage
2. definition (i.e. purpose)
3. licence info

Apologies for a lack of official term suggestion guidelines - we're volunteer run, and have to budget our time!

Split from #10.

Supernovo

https://www.proteinmetrics.com/products/supernovo/

SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery.

Proprietary commercial software licence

https://spdx.org/

Software Package Data Exchange® (SPDX®) is an open standard for communicating software bill of material information (including components, licenses, copyrights, and security references).

SPDX reduces redundant work by providing a common format for companies and communities to share important data about software licenses, copyrights, and security references, thereby streamlining and improving compliance.

The SPDX specification is developed by the SPDX workgroup, which is hosted by The Linux Foundation. The grass-roots effort includes representatives from more than 20 organizations—software, systems and tool vendors, foundations and systems integrators—all committed to creating a standard for software package data exchange formats.

This may be of interest in future versions of SWO. Should read a bit more and see how it could relate / be used.

We are developing a registry of (among other things) Earth science software and would like to be compatible with the OBO Foundry. As such, we would like to re-use as many terms as possible. We would use the SWO term for software but need it to be compatible with the sdgio ontologies resource - since softwware is a resource that can provide benefit to users. However, 3 of the many types of software under the software item include an axiom about being a "data item". This causes a logic error. The software packages are:

SAFE
Ringo
Rama

Would it be possible to remove these axioms? Also, I note that we would likely be adding a large number of subclasses for other Earth science related software packages. I don't know if you would prefer them directly added to SWO or kept in our own ontology.

Thank you!