feat: Add tool for extracting annotions of species in an ODE model #81

Rakesh-Seenu · 2025-01-29T21:27:41Z

For authors

Video3.mp4

Description

This PR introduces a new tool in Talk2BioModels that helps retrieve species annotations from a model.
When the tool is prompted tool uses get_miriam_annotation function from basico library in the backend
to retrieve the annotations of the specified species.

When this function is called, it returns the following details:

Name – The species name as recorded in the database.
URL – A link to an external database where the species is listed.
Qualifier – A category or tag that describes the species.

However, the species name is often not very informative, Hence I have developed modules that make API calls to the external databases to fetch the descriptions of the species name.
Since different species are listed in different databases, fetching their descriptions requires extra steps.

How the Tool Fetches Descriptions

The species URLs point to multiple external databases, where more detailed descriptions are available.
I have implemented three API handler files to retrieve description from specific set of databases using the provided URL.

When a user asks for a species annotation, the tool first retrieves the basic details (URL, Name, Qualifier).
Then, based on which database the species belongs to, the tool calls the appropriate API handler file to fetch its description.
Finally, all the information is displayed in an easy-to-read table.

Results Are Shown to the User is in the demo

The retrieved annotations are displayed in a scrollable table with the following columns:

Species Name : The name of the species.
Description : A brief explanation of the species from the database.
Database : The name of the database where the species is listed.
ID : A unique identifier, shown as a clickable hyperlink that directs the user to the species database page.
Qualifier : Additional information about the species annotation.

What This Tool Can Do :

✅ Retrieve annotations for one or multiple species in a model.
✅ Fetch all species annotations in a given model.
✅ Remember the model ID from chat history, so users don’t need to enter it each time.
✅ Handle errors gracefully – If a species is not found or its description is missing, the user is notified in the front end.

Upcoming Feature Enhancements

This version only allows users to view species annotations, but future updates will add more features:

Adding more Databases for API Calling
Include Databases like interpro and go
Editing & Updating Annotations
Users will be able to edit and update species annotations directly in the table.
Support for Abstract Questions
Instead of asking for specific species by name, users will be able to make broader requests, such as:
"Show me annotations of all the InterLeukins in the model ."

Fixes #57 (issue)

Type of change

Please delete options that are not relevant.

Bug fix (non-breaking change which fixes an issue)
New feature (non-breaking change which adds functionality)
Breaking change (fix or feature that would cause existing functionality to not work as expected)
This change requires a documentation update

How Has This Been Tested?

Please describe the tests you conducted to verify your changes. These may involve creating new test scripts or updating existing ones.

Added new test ( test_get_annotaion ) in the tests folder
Added new function(s) to an existing test(s) (e.g.: tests/testX.py)
No new tests added (Please explain the rationale in this case)

Checklist

My code follows the style guidelines mentioned in the Code/DevOps guides
I have commented my code, particularly in hard-to-understand areas
I have made corresponding changes to the documentation (e.g. MkDocs)
My changes generate no new warnings
I have added or updated tests (in the tests folder) that prove my fix is effective or that my feature works
New and existing tests pass locally with my changes
Any dependent changes have been merged and published in downstream modules

For reviewers

Checklist pre-approval

Is there enough documentation?
If a new feature has been added, or a bug fixed, has a test been added to confirm good behavior?
Does the test(s) successfully test edge/corner cases?
Does the PR pass the tests? (if the repository has continuous integration)

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dmccloskey

Nice work 💪. I am very pleased to see the thought that went into fetching additional information from different ontologies and databases. @awmulyadi I think the APIs could be useful for you for the enrichment part. At least chemicals, proteins, genes, GO, and diseases appear to be covered as many are included in OLS.

I have several comments in regard to the testing and how the multiple OLS sub databases are handled. Please reach out if you have any questions.

aiagents4pharma/talk2biomodels/api/kegg.py

aiagents4pharma/talk2biomodels/tests/test_api.py

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

aiagents4pharma/talk2biomodels/tools/get_annotation.py

dmccloskey · 2025-01-30T09:53:37Z

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

+        current_state = app.get_state(config)
+        dic_annotations_data = current_state.values["dic_annotations_data"]
+        print (dic_annotations_data)
+        assert isinstance(dic_annotations_data, list)


This is a good idea to test multiple models. However, simple testing that some data was created is not so rigorous. I would recommend the following on top of what you already have testing that the state data was created properly:

Prior to this test, a simple test to ensure that the outputs of prepare_content_msg are as expected.

I would use the expected string from prepare_content_msg for each of the different models for all species as the test case.

Updated the function of test_all_species which covers all the the expected outputs

Cool. However, I am still missing the test for prepare_content_msg and the comparison of the expected string produced by this method for all species (unless I somehow missed it).

reversed_messages = current_state.values["messages"][::-1] # Covered all the use case for the expecetd sting on all the species test_condition = False for msg in reversed_messages: if isinstance(msg, ToolMessage) and msg.name == "get_annotation": print("ToolMessage Content:", msg.content) # Debugging output if msg.artifact is None and ('ORI' in msg.content or "Successfully extracted annotations for the species" in msg.content or "Error" in msg.content): test_condition = True break dic_annotations_data = current_state.values["dic_annotations_data"] assert isinstance(dic_annotations_data, list),\ f"Expected a list for model {model_id}, got {type(dic_annotations_data)}" assert len(dic_annotations_data) > 0,\ f"Expected species data for model {model_id}, but got empty list" assert test_condition # Expected output is validated

Rather than using prepare_content_msg, I have added this code where it checks the expected and the tool message produced.

I see.

I think this can be made much clearer with my suggestions above.

I have created new function test_prepare_content_msg() for checking expected messages

aiagents4pharma/talk2biomodels/tools/get_annotation.py

dmccloskey · 2025-01-30T10:00:00Z

aiagents4pharma/talk2biomodels/tools/get_annotation.py

+        """
+        Process link to format it correctly.
+        """
+        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/"]


I am a bit concerned this will be difficult to maintain as there are a LOT of different ontologies. What is the problem that this method solves in regard to link formatting? If it is needed, is it possible to make it more general? Another idea would be just to include all of the ontology abbreviations from OLS if it is the same for each of them.

Problem faced is that, in Some cases the link don't work when get_miriam_annotation is called because they have database name in between the Link .

For example in model 537 for species sR

sR http://identifiers.org/pato/PATO:0001537

As the returned link is invalid, to make it a valid link i have use these substrings to remove unnecessary part in link.
yes we can include all of ontology terms, May be in next release as i don't know all the ontology abbreviations

I see. I remember running into this issue as well once...

All of the OLS abbreviations can be found here: https://www.ebi.ac.uk/ols4/ontologies.

Thanks for the link

aiagents4pharma/talk2biomodels/tools/get_annotation.py

dmccloskey

The review updates are looking much better 👍. Just a few minor comments at this point.

dmccloskey · 2025-01-31T06:40:30Z

aiagents4pharma/talk2biomodels/tests/test_api.py

-    term = "GO:ABC123"
-    label = fetch_from_ols(term)
-    assert label.startswith("Error: 404")
+    term_1 = "GO:0005886" #Negative result


Suggested change

term_1 = "GO:0005886" #Negative result

term_1 = "GO:0005886" #Positive result

I have corrected the comment

dmccloskey · 2025-01-31T06:40:44Z

aiagents4pharma/talk2biomodels/tests/test_api.py

-    label = fetch_from_ols(term)
-    assert label.startswith("Error: 404")
+    term_1 = "GO:0005886" #Negative result
+    term_2 = "GO:ABC123" #Positive result


Suggested change

term_2 = "GO:ABC123" #Positive result

term_2 = "GO:ABC123" #Negative result

I have corrected the comment

dmccloskey · 2025-01-31T06:48:36Z

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -266,10 +261,13 @@ def _fetch_descriptions(self, data: List[dict[str, str]]) -> dict[str, str]:

        # In the following loop, we fetch the descriptions for the identifiers
        # based on the database type.
+        # Constants
+        ols_ontology_abbreviations = {'pato', 'chebi', 'sbo', 'fma', 'pr'}


Much cleaner with a named variable for the abbreviations 🙂. It looks like there are two places where this list is used. Would it be possible to make this a const global variable at the top of the file or in the init so that there is no replication?

I have made it as a constant global variable

dmccloskey · 2025-01-31T07:09:43Z

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

+
+    reversed_messages = current_state.values["messages"][::-1]
+
+    # Covered all the use case for the expecetd sting on all the species


Suggested change

# Covered all the use case for the expecetd sting on all the species

# Covers all of the use cases for the expected string on all the species

I have updated the comment

…fixes

Rakesh-Seenu · 2025-02-01T09:08:39Z

Hi, @dmccloskey making some more updates I will let you know, Could you please merge the pull request after making some more changes.

dmccloskey

The updates look good 👍. Nice work 💪.

Before we can merge, please take care of the following:

the merge conflicts
open an issue for adding all of the OLS abbreviations

Rakesh-Seenu · 2025-02-03T09:42:32Z

Hi @dmccloskey, I am still working on this PR on some updates , Please review the code only after you have heard from me. Thx

Rakesh-Seenu · 2025-02-03T12:00:53Z

The updates look good 👍. Nice work 💪.

Before we can merge, please take care of the following:

the merge conflicts

open an issue for adding all of the OLS abbreviations

Hi @dmccloskey,

Thank you for your feedback. I’ve addressed the items you mentioned and would like to provide a detailed update on the recent changes:

Handling the iOS Species Return Issue:
During testing, I discovered that iOS was returning None when it should have been returning the species. I investigated the issue, implemented a fix to properly handle the case when the species needs to be returned, and added a new test case specifically for model 20. This update ensures that the behavior is now consistent and the error has been resolved.

In get_annotaion I have added below code :

In test_get_annotaion I have updated as follows :

Updating OLS Abbreviations for Model like 56:
I noticed that the [go data base] abbreviation was missing in the OLS for model 56. I’ve now added this abbreviation, and as demonstrated in the attached screenshot, it is displaying correctly.

In addition, I will open a separate issue to track the addition of all missing OLS abbreviations to ensure comprehensive coverage across models.

Additional Verifications:
I have run both pylint and coverage tests. The code meets our style guidelines, and the test coverage is complete with no conflicts, ensuring that all updates are in line with our quality standards.

Please let me know if you have any further questions or require additional changes :)

dmccloskey

Please integrate my suggestions (you may have to modify slightly), check that the tests and linting pass, and then merge 🙂.

dmccloskey · 2025-02-03T13:48:21Z

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -229,7 +234,7 @@ def _process_link(self, link: str) -> str:
        """
        Process link to format it correctly.
        """
-        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/"]
+        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/", "go/"]


Suggested change

substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/", "go/"]

dmccloskey · 2025-02-03T13:48:41Z

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -229,7 +234,7 @@ def _process_link(self, link: str) -> str:
        """
        Process link to format it correctly.
        """
-        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/"]
+        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/", "go/"]
        for substring in substrings:


Suggested change

for substring in substrings:

for substring in ols_ontology_abbreviations:

dmccloskey · 2025-02-03T13:49:24Z

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -229,7 +234,7 @@ def _process_link(self, link: str) -> str:
        """
        Process link to format it correctly.
        """
-        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/"]
+        substrings = ["chebi/", "pato/", "pr/", "fma/", "sbo/", "go/"]
        for substring in substrings:
            if substring in link:


Suggested change

if substring in link:

if substring + '/' in link:

Hi @dmccloskey ,
I’ve made the suggested updates and verified that both pytest and linting have passed successfully.

Please let me know if there’s anything else you'd like me to address.

Checks failed

dmccloskey · 2025-02-03T16:22:57Z

@Rakesh-Seenu It looks like there are a few linting failures and some failing tests. Please take a look and ping me when they have been resolved.

github-actions · 2025-02-04T09:34:26Z

🎉 This PR is included in version 1.14.0 🎉

The release is available on GitHub release

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Rakesh Hadne Sreenath and others added 17 commits January 5, 2025 20:11

added get_annotation tool

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update of annotation tool

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update of annotation tool

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latest main merge to feat-annot

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latest main merge to feat-annot

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Merge branch 'main' into feat-annot

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latest updates of feat-annot

ee06696

latest updates of error handleing

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working get_annotaions

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latest changes

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Merge branch 'main' into feat-annot

7ef53a0

latest changes

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clickable link on the id is updated

3624f4c

clickable link on the id is updated

267e2ab

code with pylint passing is being updated

45863f8

chore: update

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gurdeep330 requested a review from dmccloskey January 29, 2025 21:54

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gurdeep330 assigned Rakesh-Seenu Jan 29, 2025

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minor fixes

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gurdeep330 changed the title ~~Feat annot~~ Feat: Add tool for extracting annotions of species in an ODE model Feb 3, 2025

gurdeep330 changed the title ~~Feat: Add tool for extracting annotions of species in an ODE model~~ feat: Add tool for extracting annotions of species in an ODE model Feb 3, 2025

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dmccloskey merged commit eb27e13 into VirtualPatientEngine:main Feb 4, 2025
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	term_1 = "GO:0005886" #Negative result
	term_1 = "GO:0005886" #Positive result

	term_2 = "GO:ABC123" #Positive result
	term_2 = "GO:ABC123" #Negative result


		reversed_messages = current_state.values["messages"][::-1]

		# Covered all the use case for the expecetd sting on all the species

	# Covered all the use case for the expecetd sting on all the species
	# Covers all of the use cases for the expected string on all the species

	for substring in substrings:
	for substring in ols_ontology_abbreviations:

feat: Add tool for extracting annotions of species in an ODE model #81

feat: Add tool for extracting annotions of species in an ODE model #81

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Rakesh-Seenu commented Jan 29, 2025 • edited Loading

For authors

Description

How the Tool Fetches Descriptions

Results Are Shown to the User is in the demo

What This Tool Can Do :

Upcoming Feature Enhancements

Fixes #57 (issue)

Type of change

How Has This Been Tested?

Checklist

For reviewers

Checklist pre-approval

Checklist post-approval

Checklist post-merge

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