ontologies | Ontology Repository for http : //onto.ir | User Interface library

by morteza Java Version: Current License: No License

X-Ray Key Features Code Snippets(1)Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | ontologies Summary

ontologies is a Java library typically used in User Interface applications. ontologies has no bugs, it has no vulnerabilities and it has low support. However ontologies build file is not available. You can download it from GitHub.

Ontology Repository for

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Support

ontologies has a low active ecosystem.

It has 9 star(s) with 1 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

There are 0 open issues and 1 have been closed. On average issues are closed in 27 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ontologies is current.

Quality

ontologies has 0 bugs and 0 code smells.

Security

ontologies has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

ontologies code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ontologies does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

ontologies releases are not available. You will need to build from source code and install.

ontologies has no build file. You will be need to create the build yourself to build the component from source.

ontologies saves you 18 person hours of effort in developing the same functionality from scratch.

It has 51 lines of code, 3 functions and 3 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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ontologies Key Features

No Key Features are available at this moment for ontologies.

ontologies Examples and Code Snippets

Retrieve all ontologies

java

Lines of Code : 4

License : Permissive (MIT License)

Copy

public static List retrieveTodos(String user) {
		throw new RuntimeException("Database Down");
		// return Arrays.asList("Learn Spring","Learn Struts","Learn to Dance");
	}

Community Discussions

Trending Discussions on ontologies

Beginner guide to omics data warehousing

How to access the child elements of an element with minidom?

How To Set Fetch Data In to Array Using JavaScipt And Set Data In To innerHTML Boostrap card

How to create a lattice-type data structure in Haskell?

JavaScript fetch() with JSON parameter

Object Properties with disjoint classes in Protege

SPARQL CONTRUCT ordered list with ORDER BY and GROUP BY

Custom functions in a SPARQL BIND expression in JENA

OWL reasoning based on subset of relationships

insert data to Fuseki with sparql query

QUESTION

Beginner guide to omics data warehousing

Asked 2021-May-25 at 19:26

I work in bioscience field, mainly involved in data analysis. Lately, numbers are growing and things are getting more complicated by the use of multiple analysis techniques (most of them "omics" type) on various biological samples from the same set of individuals/patients/animals.

I would like to implement a better way of locally storing data and meta-data (here I refer to meta-data as the general data about the individuals/patients/animals, but also to meta-data about instrument used in assay) which would also allow me to perform meta-analysis (mainly using R, but I would like to have a solution that can also work with SPSS). I am searching for some guides to learn the basics of building, managing and using databases, optimally tailored to biology and "omics"application.

I could summarize my situation in the following image

In summary, over the same set of samples (individual - S1 to Sn), that would be the main entry in the database, we could perform a series of experimental assays, each of which resulting in some numeric data generally organized in a csv like format with the same id, accompanied by some meta data about the assay (instrument used and similar). The creation of new entries in the database would usually be via bulk upload of those csv files.

Essentially, I would like to collect and connect everything in one place, instead of having 1 folder for every project, with related R script and raw data. From R, I would then retrieve from the general database the data relevant to a certain project, and perform a set of analyses. As of now, I am interested in a local solution, but I would like to leave the eventual predisposition for remote access open

I have no background in databases, so I am open to any solution which would better fit my needs. For example, I have read that there are relational databases and graph databases (I do have some experience with ontologies) and can't decide which would be better. Any "digested" source of general information from users who have handled similar issues, any beginner tips, or any suggestion on best solution, would be of great benefit for me to try and start something.

...

ANSWER

Answered 2021-May-25 at 19:26

Actually, I disagree with the commenters who are criticizing this question, though I agree it is not specific to R or R-related programming. Maybe I just sympathize because I have been in a similar position. A better venue to ask something like this might be BioStars.

That said, I also work in academia, and I also had a similar problem. No one in my circles had a great answer.

From your diagram, it seems like you know something about relational databases, which is good. If you aren't familiar with sql-like syntax or relational database ideas, then definitely start there. I don't have a great suggestion on how to learn about these -- I had a class on mysql in college, and then started using sqlite and postgresql on my own. I very much appreciated the mysql class, so if you feel like you don't know sql-like syntax or relational database topics well, maybe you could find an online course (or take one at your university, if you are located at a school).

Specifically in R, I would start reading about connecting to a database from R/Rstudio

https://db.rstudio.com/

I use this predominantly through the RPostgresql package, which is an extension of the DBI package, I think.

Obviously get very comfortable with the tidyverse packages, if you aren't already. This is a great resource:

https://r4ds.had.co.nz/

Since we're on the topic of Hadley Wickham, and since the topic of Hadley Wickam is related to R and R-programming, I don't feel bad saying you should read this, too:

https://vita.had.co.nz/papers/tidy-data.pdf

You'll need to learn some basics about servers. I understand that you're specifically interested in doing this locally, but I suspect that there will come a time that you'll need to be able to both host locally and remotely. At least, that has been my experience. In any case, you should be using linux (I hope this isn't too contentious a statement) on your local computer, which means essentially that dealing with a local database is more or less the same as dealing with one remotely (minus some security concerns). I find Nginx easier than Apache, but that is likely a matter of taste. I use Amazon AWS when I need a public server, though if your university has hosting services, you could do a price comparison. AWS has been cheaper and easier in my experience. To manage a served database, I use Django, which is a python package. If you choose to build a django managed database, I suggest using this cookiecutter (a python package template):

https://github.com/agconti/cookiecutter-django-rest

Finally, posted below is a link to a django database framework for a currently active project for which I'm managing the data. I'm going to include another link to a R package that I'm also messing around with, which is meant to absorb some of the database data, process it, and spit it out. The latter is very much under development. It isn't in a share-able state, but it would have helped me to see something like this, I think, when I started asking similar questions to yours, so I'm going to include it.

https://github.com/BrentLab/S288CR64_database

https://github.com/cmatKhan/brentlabRnaSeqTools

If you have questions specifically related to genomics data management, feel free to ask via my email. You'll find it on github.

Source https://stackoverflow.com/questions/67531163

QUESTION

How to access the child elements of an element with minidom?

Asked 2021-May-24 at 06:46

I am reading an XML/OWL file (generated from Protege) in Jupyter notebook.

I can read the root element, but for children its showing error/blank.

...

ANSWER

Answered 2021-May-24 at 06:46

You have this structure

Source https://stackoverflow.com/questions/67667051

QUESTION

How To Set Fetch Data In to Array Using JavaScipt And Set Data In To innerHTML Boostrap card

Asked 2021-Apr-26 at 15:00

I Have Fetch Methord Like This.

...

ANSWER

Answered 2021-Apr-26 at 14:52

I think what you need from the API are the recipes, so the API returns them in the hits property. The hits property is an array of recipes

The properties in the recipe object are; SO you can pick what you need,

Source https://stackoverflow.com/questions/67268458

QUESTION

How to create a lattice-type data structure in Haskell?

Asked 2021-Apr-19 at 21:51

I am trying to build a lattice-type of FCA-type of data structure in Haskell where I could check if two entities have a join or not. Actually, I'm not even sure that the lattice is the right structure as it might be a bit "too much".

Here is the context. In a COBOL program analyzer, I have an ontology of data set names, files, records and fields. A data set name can have multiple file names depending on the program, a file can have multiple records and a record can have multiple fields. I'd like this hierarchy to be reflected in the Haskell data structure. But I'd like also to be able to have a relation inherited for file1 and file2 such that I can check if file1 and file2 belong to the same data set name. Actually, this relation could almost be that of "==". But it could simply be that they do have a join in dsn0, for instance.

I have other ontologies in that context that would benefit from a lattice or FCA data structure. For example, I have programs that belongs to job steps and job steps that belong to jobs. If I could easily figure out if two programs belong to the same job, that would be great. Here also, it seems like a "join" operator. Getting the extension (code) of a certain entity would be useful too.

I'm still a bit new to Haskell. I tried to look at the Lattice library but I'm not sure where to go from there, concretely. Any idea of how to get started? A small example of a lattice in Haskell would be very helpful. Thank you very much for your help (and patience).

UPDATE: The Lattice might not be the best formalism for this as mentioned in the comments. I realize I might just have to use a regular class type of data structure along those lines:

...

ANSWER

Answered 2021-Apr-19 at 21:51

I recommend making an abstract data type to represent one-to-many relationships. It might look something like this:

Source https://stackoverflow.com/questions/67154132

QUESTION

JavaScript fetch() with JSON parameter

Asked 2021-Mar-22 at 00:17

I'm attempting to request nutrients from the Edamam Food Nutrition api using Node.JS. They provide this example using curl curl -d @food.json -H "Content-Type: application/json" "https://api.edamam.com/api/food-database/v2/nutrients?app_id=${YOUR_APP_ID}&app_key=${YOUR_APP_KEY}"

I've successively fetched data from their Food Database API where the only parameter is a URL. This one is requires a JSON with the URL. I've hard coded a JSON to correctly call the API. The response I get is

{ "error": "bad_request", "message": "Entity could not be parsed" }

What needs to be changed to get a good response?

...

ANSWER

Answered 2021-Mar-16 at 00:50

Your data myFood already is a JSON string, then no need to cast it to string with JSON.stringify(data) in postData function.

A simple way to fix this issue - make sure the data object always be a JSON object.

Source https://stackoverflow.com/questions/66647622

QUESTION

Object Properties with disjoint classes in Protege

Asked 2021-Feb-23 at 14:21

I would like to model an ontology where I can represent an absence of entity so to say. I want for example to have Rain and No_Rain, which I would define as disjoint classes. After this I have the object Property has_rain. I want somehow to be able to reason that it's not possible to have at the same time for the same individual has_rain(Rain) and has_rain(No_Rain) I've searched a lot and couldn't find the answer to my problem. Maybe I've missed it somewhere. Sorry if I didn't explain everything good, this is my first question. I hope you understood everything and thanks in advance! Edit:

...

ANSWER

Answered 2021-Feb-23 at 09:47

EDIT: This is actually wrong, to do it this way.

Okay actually I somehow managed to fix my problem :D If you define the object property as functional and then try to connect an individual with both rain and no_rain, then the reasoner tells you it's inconsistent, which was what I needed. I would still be happy if someone says, if this is the correct way to model it. enter image description here

Source https://stackoverflow.com/questions/66314597

QUESTION

SPARQL CONTRUCT ordered list with ORDER BY and GROUP BY

Asked 2021-Jan-10 at 15:02

Dear RDF/SPARQL community,

my goal is to construct an ordered list grouped by products and ordered by time by the means of SPARQL to show the track of a product. I am working with GraphDB, "scmon" is my custom ontology. And here are the details:

I have stored RDF data that hold the timestamps (scmon:atTime) and positions (scmon:atLocation) of products. In Turtle syntax it looks like this:

...

ANSWER

Answered 2021-Jan-10 at 15:02

This way:

Source https://stackoverflow.com/questions/65628046

QUESTION

Custom functions in a SPARQL BIND expression in JENA

Asked 2021-Jan-06 at 16:11

I want to use custom functions in BIND expressions in Jena, but it does not work.

To take a small example, I have an Owl ontology with one Human class, having the following int data properties:

Age
BirthDate

My query is the following:

...

ANSWER

Answered 2021-Jan-06 at 16:11

My mistake was:

Source https://stackoverflow.com/questions/65599184

QUESTION

OWL reasoning based on subset of relationships

Asked 2020-Dec-24 at 08:27

I have the following example instance of the Brick.ttl buildings ontology

...

ANSWER

Answered 2020-Dec-24 at 08:27

In the Manchester syntax, instead of

Source https://stackoverflow.com/questions/64996700

QUESTION

insert data to Fuseki with sparql query

Asked 2020-Nov-04 at 21:52

I am trying to insert new data to Fuseki through SPARQL query, it's giving me success(200 OK) but it's not showing in my TDB. and I think it's because I haven't defined to which graph but I don't know-how

...

ANSWER

Answered 2020-Nov-04 at 21:52

try to reformat your queryString as shown in this picture.

reference

be careful where to close your subject
"PREFIX ns:" <== is already closed, while you need to insert your d.getDomainName() before closing ">"

Source https://stackoverflow.com/questions/64676091

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install ontologies

You can download it from GitHub.
You can use ontologies like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the ontologies component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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