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github.com/Bioprotocols/container-ontology

Container ontology for use with PAML (Protocol Activity Markup Language)
https://github.com/Bioprotocols/container-ontology

merge ignore

e699f03d13f858606484e097f15f9f71f36e34d6 authored about 2 years ago by Daniel Bryce <[email protected]>
ignore egg files

cc1c55c7752ef20e7602027cc82d7271d752497a authored about 2 years ago by Daniel Bryce <[email protected]>
Merge pull request #39 from photocyte/main

Create LICENSE.md

bda7ca04c8884d457724a819123835c6ebb5552b authored over 2 years ago by Jacob Beal <[email protected]>
Update LICENSE.md

Added requested changes on credit

ba10055d01f0b8cb2daff0bd751206768a856245 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Update LICENSE.md

Instructions say not to include the brackets. Removing.

b18f41a6d6714e1bc5015e181e260aa08cddebc2 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
Create LICENSE.md

Add Apache 2.0 LICENSE.md with "2022 Bioprotocols Working Group"

445f56ad32f082dc42b4963063cb0b732491e794 authored over 2 years ago by Timothy R. Fallon, PhD <[email protected]>
fix link to Owlery API docs

72b8b2f6af391e41032e915fa011e49df42c944c authored over 2 years ago by James Scott-Brown <[email protected]>
Get owlery-client from git repo. (#23)

Remove the owlery-client, automatically generated from the spec, to a separate repo, from which ...

ff1d61e93bb75995c2144b3996f5a6d9a788d6b6 authored almost 3 years ago by rpgoldman <[email protected]>
Add note about the GitHub Discussions.

Try to point readers to the Discussions tab for Q&A.

d39b6326d4b5ece6fa754a9c391add1bf89ca47d authored almost 3 years ago by rpgoldman <[email protected]>
Fix imports for owlery_client.

Previously, sub-modules were not imported.

1af1623e06494670c9a5cb1e0a653b39e6ca386f authored almost 3 years ago by Robert P. Goldman <[email protected]>
Update the Makefile with fixes needed for new Docker image.

f5b052d5a3abfb2e3443920c73016bd21f367a1e authored almost 3 years ago by Robert P. Goldman <[email protected]>
Title image with icon from Noun Project (#14)

When I was migrating this repo from my personal GitHub account to Bioprotocols, I was prompted t...

9869793e2566714c2c75ff6e2eae22f4d05a7d77 authored almost 3 years ago by rpgoldman <[email protected]>
Remove obsolete Makefile rule.

a9276d29e07bfc3ca7899b9fbbe6b1d715f33bf1 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Remove old m4 file.

c1ba40508eb292b34510e999a0a21b03718e8a00 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Update owlery catalog of ontologies.

Use .omn (OWL Manchester notation) in place of Turtle file.

50290a1fa05a6e2cc5ad9ab371caf4472eb9aa25 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Improved and simplified Owlery service configuration.

4cbf815dd9fbe43f2500642292dd387a13c2b324 authored almost 3 years ago by Robert P. Goldman <[email protected]>
Improved the documentation.

ec9c0d08a8091b8339f8c3ba3dbc77474fccc9dd authored almost 3 years ago by Robert P. Goldman <[email protected]>
Merge pull request #12 from rpgoldman/merge-client-package

This merge pulls in a branch that is a cleaned-up version of the client-package, which has an ug...

a7dd08801bbbf5659966002db12e227d64a7a845 authored about 3 years ago by rpgoldman <[email protected]>
Update the ontology for the server.

- Add a local copy of SBOL3 to the server.

- Make `hasWellBottomShape` a functional property. ...

2aefad6bec9a413c391f02a798ae14f554891b15 authored about 3 years ago by Robert P. Goldman <[email protected]>
Add instructions for install and use.

d4eab7e31e5af7b34bb82dfe58ff88e4530568fe authored about 3 years ago by Robert P. Goldman <[email protected]>
Client API for container ontology server.

The client API has two components:
1. Auto-generated API to the Owlery container server, based o...

f00bc37ca2fa3c3c1e8cfc7d4ee9731cc3bab9f2 authored about 3 years ago by Robert P. Goldman <[email protected]>
More info on Strateos catalog.

38ca3d9148bdf024c63ca78b5e2f8ce99f7b17db authored about 3 years ago by Robert P. Goldman <[email protected]>
Fix use of wrong OM property.

Had mistakenly used `hasDimension` where I should have used `hasUnit`.

0bc4d2518affbbff5637c57d77933af3e8614cb0 authored about 3 years ago by Robert P. Goldman <[email protected]>
Update catalog of OWL files.

0f0affe5fb967b164596217a111caa2f299d8234 authored about 3 years ago by Robert P. Goldman <[email protected]>
Replace xsd:float with xsd:decimal.

xsd:float is disjoint with all other numeric types, unlike xsd:decimal, so we are using that as ...

264095450722a78a87e1dc7d269f96449d6b3ba6 authored about 3 years ago by Robert P. Goldman <[email protected]>
Test ability to run owlery server.

c0bfa46b3ec1af6790625487aaf45c4afd8956f4 authored about 3 years ago by Robert P. Goldman <[email protected]>
Add more shape and color properties to Strateos catalog.

109c55775cc62c9215ce8679dd13039bdb2a7b53 authored about 3 years ago by Robert P. Goldman <[email protected]>
Updates to container ontology.

1. Connect the cont:Plate class with the NCIT class for Microwell Plate
2. Add cont:NotFlatWellB...

dd1633295b6d461e44a8d68437fa40599f083bf7 authored about 3 years ago by Robert P. Goldman <[email protected]>
Replace temporary IRI prefix.

Previously I was using https://raw.githubusercontent.com/rpgoldman/container-ontology/main/owl/ ...

944e29aec95bd6a8fee32ec2df9776b9a1b3c406 authored about 3 years ago by Robert P. Goldman <[email protected]>
Fix loading redirect.

2d93bc72dcd07f9693a2f2b4a09ac14a83565a57 authored about 3 years ago by Robert P. Goldman <[email protected]>
Update NEST PCR plate description.

2904bf38550f3eae083e8c99ebe5ffe8062ea304 authored about 3 years ago by Robert P. Goldman <[email protected]>
Extensive restructuring of container ontology. (#10)

ec387d70d47c72aeb672caaf5a8d31e3268bce03 authored about 3 years ago by rpgoldman <[email protected]>
Add small BBN lab catalog.

d7ad301ce7cf910ee804e4e8fd98af7b43aa1637 authored about 3 years ago by Robert P. Goldman <[email protected]>
Add volume measurement info.

954a20371e2cf20894624bdbba75dc73d3e90cc3 authored about 3 years ago by Robert P. Goldman <[email protected]>
Update server configuration.

Use my own copy of the Owlery docker image to ensure compatibility.

70671d37e4615042eed19ee08b724023af325fb5 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add catalog file.

Jim Balhoff suggests loading the main ontology (here strateos-catalog-individuals.ttl) and letti...

b0667f7fa8bcda5758b366e6da40843ae22fbbff authored over 3 years ago by Robert P. Goldman <[email protected]>
Reset ontology IRI to main branch.

Was on `owlery-server` branch, which has been deleted.

806706e60974024f73f7dea74edde0aadb32067c authored over 3 years ago by Robert P. Goldman <[email protected]>
Add logging.

Add JAVA_ARGS to Makefile invocation of docker image for logging.
Also tee the logging output to...

8be8913ee96736741325f2d47d69214a6a7e350e authored over 3 years ago by Robert P. Goldman <[email protected]>
Add more instructions for the server.

36a31d35b11a593e0f0162ae7d5ea8301b575cce authored over 3 years ago by rpgoldman <[email protected]>
Add an Owlery server (#9)

Owlery provides a server that can incorporate a knowledge base of OWL ontologies and respond to ...

8f8006dc67594d781c09dbbba00b4be603a0988b authored over 3 years ago by rpgoldman <[email protected]>
Update ontology URIs for main branch.

ca4a80f8311d07d90f22685107754cc345a858e6 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add Makefile for relocating the ontology.

0e4292cb4471a49b9d6cb6932a19a4a073ea1883 authored over 3 years ago by Robert P. Goldman <[email protected]>
Merge pull request #8 from rpgoldman/iss7

291ef0376a9bf6747fdbd109de14946ee7704713 authored over 3 years ago by rpgoldman <[email protected]>
Branch-specific OWL catalog.

c165c96a416c0eb1989ab06db9186f9b20872048 authored over 3 years ago by Robert P. Goldman <[email protected]>
Commit branch-specific TTL files.

This is an ugliness made necessary by the fact that the files must
have their own URL in them. ...

cd296ecaad1f84e630b7e67861d6c1edcd1651bb authored over 3 years ago by Robert P. Goldman <[email protected]>
Use M4 to store ontology files.

Need to be able to put the ontology files at temporary locations that
vary based on the git branch.

dba0afcc8267df9267906392092641760d0513a6 authored over 3 years ago by Robert P. Goldman <[email protected]>
Store old copy before changes.

2df28524989393a3dbdc58f354daa91abb10f6b5 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add ability to record availability.

Add the `availableAt` property and the `Lab` class to fill that property. This will allow us to...

80a1a88d056bcdeac0eda77698348ff9f41acb82 authored over 3 years ago by Robert P. Goldman <[email protected]>
Improve ignores.

468fb40efaf0e2b6cd44010458709ef98ee58f4d authored over 3 years ago by Robert P. Goldman <[email protected]>
Add source format of Strateos Catalog.

cc6c5701bab8ac1c28107497180af6a8122e4fa0 authored over 3 years ago by Robert P. Goldman <[email protected]>
Refine the model and translator.

Fixed the definition of Standard96WellPlate to be more useful.
Also fix some translator errors.

b41667297cae36600e5d9c1e9a1b608c794427b1 authored over 3 years ago by Robert P. Goldman <[email protected]>
Make two different catalog versions

One has the catalog entries as classes, and one as individuals. The latter supports more efficie...

d048860476a5e843c34d803c1e2f67edf09f3e86 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add standard 384- and 1536-well plate.

0f82a13b048d4a50871822d81e81c87cbb754b97 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add catalog_translator python module

This is not yet properly packaged, but works to the extent that it's
worth sharing.

800346e9fa739dd02eedf17f3e9182e5b7f21f36 authored over 3 years ago by Robert P. Goldman <[email protected]>
Replace Individuals with Classes.

Previously, translated catalog entries in the Strateos catalog into
Individuals, with property a...

6f1cfc542bcd0c8071f7eee228cefd46019f82e6 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add standard classes.

ae2164b33581e9e5ae2b894fdc1cf5d3cf19d011 authored over 3 years ago by Robert P. Goldman <[email protected]>
Improve translator Strateos catalog to OWL.

a596b2163c2c117ee7f467458b0b0a3278e81005 authored over 3 years ago by Robert P. Goldman <[email protected]>
Change IRI and add fixes.

For now I gave the ontology a routable name -- even if a stupid one -- because I have been havin...

db3687fc37b63d1c8860460d7454b8121ebd9ed1 authored over 3 years ago by Robert P. Goldman <[email protected]>
Replace misnamed file.

Turtle file had `.owl` extension, instead of `.ttl`.

600f9a372fa80fd1be4308ccfd1e711e40661642 authored over 3 years ago by Robert P. Goldman <[email protected]>
Hand-repaired auto-generated file.

857f5483f94264b8b2d0d88562959de45c5553a0 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add colors for optical properties.

These were one of the properties that the group called out as most important.
Replaced the `Opti...

4276adc3be17f6672fe95cf6e81c86efd5ac3691 authored over 3 years ago by Robert P. Goldman <[email protected]>
Replace volume with wellVolume.

Make it more clear what is intended by the `volume` property.

047863bcaaff965ec75112a9124d6a24b5ae3085 authored over 3 years ago by Robert P. Goldman <[email protected]>
Notebook for translating plate data to OWL classes.

3b9e422499e99a5f070559b5b07f37204c9f006a authored over 3 years ago by Robert P. Goldman <[email protected]>
Plate classes from the Strateos catalog spreadsheet.

27dde5737dfaf1aa96bbe3faa9027ab9ced5a294 authored over 3 years ago by Robert P. Goldman <[email protected]>
Notebook for translating plate data spreadsheet.

21c76a01b52e20c727f77c18a118ff62f1a1e480 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add ThermoFisher plates by hand.

e4ca94fed54dcc27cce10782658ad26b2b5bb632 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add well properties.

Add `hasWellShape` and `hasOpticalProperty`.
Fixed minor bugs:
* the label of the `length` prop...

2380655ca2540e09ac2fad10ea6dba9d1161960c authored over 3 years ago by Robert P. Goldman <[email protected]>
Script for diffing versions of container ontology

56d19c602b887a2b5aaab2900c150ce2e794de14 authored over 3 years ago by Robert P. Goldman <[email protected]>
Multiple fixes to container ontology

Removed spurious disjoint properties
Recorded properties that were functional
Added three subcla...

f7f04e5afd07c7897c4ae6f89e9a24cbdc05c96e authored over 3 years ago by Robert P. Goldman <[email protected]>
Ignore PyCharm and Mac metadata.

444ad1ffde53ae2b0b58228722e6c352b3af9547 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add missing rdfs:label properties.

Automatically scanned over the ontology and added `rdfs:label` properties
to classes that didn't...

9e33e353676e7a4a7d332e69f51ffe29efbc130c authored over 3 years ago by Robert P. Goldman <[email protected]>
Put container-ontology in rdflib canonical form.

Read container ontology into rdflib and then serialize it.
I hope that this will make further di...

18f8e7a8e00acb266d0fdc4cd26c4b07e7668583 authored over 3 years ago by Robert P. Goldman <[email protected]>
Extend for SBOL-factory compatibility

Added a `ContainerRoot` class to (optionally) inherit from `sbol:Identified`.
Add `rdfs:label` f...

85ce1f35af2c8388358935c0659691d323529657 authored over 3 years ago by Robert P. Goldman <[email protected]>
Add ANSI/SLAS standards.

Add classes for ANSI/SLAS x-2004 standards for multi-well plates.

58e01a572a7cd18e43270630ad57db0f346b66bc authored over 3 years ago by Robert P. Goldman <[email protected]>
Fixes to Miles Rogers' microplate example.

eed589d3290a476cc3e0c44dd8969e5ea6eef599 authored over 3 years ago by Robert P. Goldman <[email protected]>
First translation of a spec from Miles Rogers.

ca69d4ba46a165a81eae2f6bcf50929bb8536b4c authored over 3 years ago by Robert P. Goldman <[email protected]>
First, partial draft.

9767093cde6397860bc9472950b8d99027d3af55 authored over 3 years ago by Robert P. Goldman <[email protected]>
Update README.md

Some initial description and links.

b4e826d0b48ad21ba5210f703f696e36bd78334f authored over 3 years ago by rpgoldman <[email protected]>
Initial commit

5e623488bae51c75dc184ae441fc8bf55e431d6b authored over 3 years ago by rpgoldman <[email protected]>