pride-utilities / pride-ontology

The PRIDE ontology

pride-utilities

About PRIDE Utilities

The primary purpose of PRIDE Utilities library is to provide commonly used classes shared by all the PRIDE Tool Suite. You may also find it useful for your own computational proteomics projects.

License

pride-utilities is a PRIDE API licensed under Apache License 2.0.

How to cite it:

Perez-Riverol, Yasset, Julian Uszkoreit, Aniel Sanchez, Tobias Ternent, Noemi del Toro, Henning Hermjakob, Juan Antonio Vizcaíno, and Rui Wang. "ms-data-core-api: an open-source, metadata-oriented library for computational proteomics." Bioinformatics 31, no. 17 (2015): 2903-2905. ms-data-core-api

Main Features

• Data Structures to represent AminoAcids, Mass Table, etc.
• Functions to compute different Properties such as isoelectric point, retention time, sequence length and masses.
• Reference table of the main Ontology terms used in PRIDE-toolsuite.
• General functionalities and data structures classes missing in JDK, such as: Tuple.
• General functionalities like checking email format and availability.

The library provides four key modules:

• mol: contains classes describing entities at the molecular level, such as: amino acids, neutrual losses, peptides and fragment ions.
• gui: contains several GUI components, you can use them if you want to replicate some of the features in PRIDE Inspector.
• data: contains data structures classes are missing from JDK, such as: Tuple.
• util: contains a selection of convenient classes. For examples: for formatting protein related informations, for checking Internet availability or for verify email addresses.

Note: the library is still evolving, we are committed to expand this library and add more useful classes.

Getting PRIDE Utilities

The zip file in the releases section contains the PRIDE Utilities jar file and all other required libraries.

Maven Dependency

PRIDE Utilities library can be used in Maven projects, you can include the following snippets in your Maven pom file.

 <dependency>
   <groupId>uk.ac.ebi.pride.utils</groupId>
   <artifactId>pride-utilities</artifactId>
   <version>0.1.23-SNAPSHOT</version>
 </dependency> 

 <!-- EBI repo -->
 <repository>
     <id>nexus-ebi-repo</id>
     <url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo</url>
 </repository>
 
 <!-- EBI SNAPSHOT repo -->
 <snapshotRepository>
    <id>nexus-ebi-repo-snapshots</id>
    <url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo-snapshots</url>
 </snapshotRepository>

Note: you need to change the version number to the latest version.

For developers, the latest source code is available from our SVN repository.

Getting Help

If you have questions or need additional help, please contact the PRIDE Helpdesk at the EBI: pride-support at ebi.ac.uk (replace at with @).

Please send us your feedback, including error reports, improvement suggestions, new feature requests and any other things you might want to suggest to the PRIDE team.

This library has been used in:

• Wang, R., Fabregat, A., Ríos, D., Ovelleiro, D., Foster, J. M., Côté, R. G., ... & Vizcaíno, J. A. (2012). PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nature biotechnology, 30(2), 135-137. PDF File, Pubmed Record

• Côté, R. G., Griss, J., Dianes, J. A., Wang, R., Wright, J. C., van den Toorn, H. W., ... & Vizcaíno, J. A. (2012). The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Molecular & Cellular Proteomics, 11(12), 1682-1689. PRIDE Converter 2

• Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., ... & Hermjakob, H. (2013). The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic acids research, 41(D1), D1063-D1069. PRIDE-Archive

• Perez-Riverol, Y., Xu, Q.W., Wang, R., Uszkoreit, J., Griss, J., Sanchez, A., Reisinger, F., Csordas, A., Ternent, T., del-Toro, N. and Dianes, J.A., 2016. PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets. Molecular & Cellular Proteomics, 15(1), pp.305-317. PRIDE Inspector Toolsuite

How to use pride-utilities

Using PRIDE-Utilities

Here we will show you how to use the PRIDE Utilities library to calculate m/z delta and calculate theoretical mass of a given peptide.

Calculate m/z Delta:

You can find the method for calculating m/z delta from MoleculeUtilities in uk.ac.ebi.pride.mol package. It requires four input parameters:

/*
 * sequence is the peptide sequence in String,
 * precursorMz is the precusor m/z in double,
 * precursorCharge is the precursor charge in double,
 *ptmMasses is a list of post translational modifications in double.
*/

// Direct call on the method
Double mzDelta = MolecularUtilitites.calculateDeltaMz(sequence, precursorMz, precursorCharge, ptmMasses);

Calculate Theoretical Mass

You can also find the method for calculating theoretical mass value from MoleculeUtilities. It needs two input parameters:

 /*
  *sequence is the peptide sequence in String,  
  *masses is a optional list array of masses you want to add as extras.
  The following lines of code shows you how:
 */

 // Direct call on the method
 double result = MolecularUtilitites.calculateTheoreticalMass(sequence, masses);

 // Tip: Take a close look at other methods within MoleculeUtilitites, you might find them useful. 

pride-ontology's Issues

Missing terms for TMTpro 18-plex reagents

Could support be extended for TMT134C and TMT135N labels as was done in #70 for TMT 16-plex?

Happy to submit a PR if that's easier.

Obo term for ion mobility based fractionation

Hello,

I'm currently annotating the SDRF for this project (PXD020785). I'm wondering what term I should use for the fractions separated by Differential Mobility Separation on a SelexION device. Can you help me here?

Kind regards,
Caro

SyntaxError: expected QuotedString

That's in line 2926:

def: Studying all protein samples of diverse host environments like the human body, soil or sea water. [PRIDE:PRIDE]

Same in 2935 and some

Problem with tag

This tag Human Proteome Project, Sars-CoV-2, Covid-19 is the combination of three existing tags. Can we remove it. @deeptijk @javizca

https://github.com/PRIDE-Utilities/pride-ontology/blob/master/pride-annotations/project-tags.csv#L31

rq: new experiment type - quality control

@ypriverol You can assign that to me

Regenerate OWL file

The OWL file needs regenerating from the new OBO file that has new terms.

Addition of TMT channels to PRIDE controlled vocabulary: 133N, 133C, 134N

Hello,

Can you add TMT channels, TMT133N, TMT133C and TMT134N to the accepted TMT labels within the PRIDE controlled vocabulary? I am using a TMT16plex which has additional channels not found in the ontology at this time.

Thank you,

Danielle Weise

Add new Project Tag "Shotgun proteomics"

Hey !
Could you please add the project tag "Shotgun proteomics" ?
Thank you.

Kind regards,
Anika

Problem parsing pride OWL file

Can't read the OWL file with the OWL API, parsed complained about a URI syntax exception in line 798 here

Not a subclass of experiment type: shotgun proteomics

As seen e.g. in a submission.px
MTD experiment_type [PRIDE, PRIDE:0000429, Shotgun proteomics, ]

SyntaxError: expected XrefList

That's in line 3310:

def: "Accession or Code of the individual in the sample"

syntax error in pride_cv.obo

The part_of syntax for these terms is incorrect:

[Term]
id: PRIDE:0000593
name: CID collision energy
def: "CID collision energy"
is_a: MS:1000045 ! collision energy
part_of: id: PRIDE:0000591 ! CID

[Term]
id: PRIDE:0000594
name: HCD collision energy
def: "HCD collision energy"
is_a: MS:1000045 ! collision energy
part_of: id: PRIDE:0000590 ! HCD

[Term]
id: PRIDE:0000595
name: EThcD collision energy
def: "EThcD collision energy"
is_a: MS:1000045 ! collision energy
part_of: id: PRIDE:0000589 ! EThcD

[Term]
id: PRIDE:0000596
name: ETciD collision energy
def: "ETciD collision energy"
is_a: MS:1000045 ! collision energy
part_of: id: PRIDE:0000592 ! ETciD

correct syntax should be:

relationship: part_of PRIDE:0000591 ! CID

PRIDE/Unimod ontology needs to be included in OLS4

• Find a way to convert obo -> owl.
• Store the Unimod Ontology file sync with Unimod.
• Test the new ontology in OLS4.

SyntaxError: expected XrefList

.obo format not observed. related to #17

  File "/tmp/pride-ontology/pride_cv.obo", line 3386
    def: "Quantification channel label"␊
                                       ^
SyntaxError: expected XrefList

Resolving "Project Identifier" URI

It seems like Pride URI's like for "project identifier" aren't resolving to purl.obolibrary.org/obo/ - and part of that would be because the controlled vocab. isn't listed in OBOFoundry.org. Is there a plan to get it in place; as well what is the ontology curation support at this point? Or is there a plan to change the URI? They really should resolve...

Thanks,

Damion

BioPortal submission

I was wondering if you would mind adding the PRIDE ontology to BioPortal? Or if there is a specific reason it is not added yet? I know the ontology is well accessible via your own OLS, but we are currently using the ISAcreator from the ISA-tools suite to manage our metadata. And as far as I'm aware it only connects with BioPortal. I think adding the PRIDE ontology to BioPortal would also probably benefit your reach and application. I would be glad to add it myself, if I get the permission to do so.

suggest to remove "Human Proteome Project, Sars-CoV-2, Covid-19" project tag

We have a tag "Human Proteome Project, Sars-CoV-2, Covid-19" which I believe incorrect and should remove from here. because it should be three different tags which are already in the list: Human Proteome Project, Sars-CoV-2and Covid-19

Add version to OWL and OBO files

Right now, PRIDE is among a small group of ontologies in the Ontology Lookup Service that don't report a version nor a version IRI.

2021-12-20 10:11:41 DEBUG    [co_326] no OLS version
2021-12-20 10:11:41 DEBUG    [co_336] no OLS version
2021-12-20 10:11:41 DEBUG    [co_359] no OLS version
2021-12-20 10:11:41 DEBUG    [fideo] no OLS version
2021-12-20 10:11:41 DEBUG    [fobi] no OLS version
2021-12-20 10:11:42 DEBUG    [one] no OLS version
2021-12-20 10:11:42 DEBUG    [pride] no OLS version
2021-12-20 10:11:43 DEBUG    [xl] no OLS version
2021-12-20 10:11:43 DEBUG    [xlmod] no OLS version

It would be great if this could be added