Add literature utils

[cthoyt]

This PR adds a workflow for searching literature, retrieving abstracts, annotating them, and summarizing the results.

Specifically, it's a demo of how you can quickly re-use the pre-defined lexica. For example, querying for diabetes (limited to 300 recent articles) and grounding using the phenotype lexicon in the following code gives:

from biolexica import load_grounder
from biolexica.literature import annotate_abstracts_from_search
from biolexica.literature.analyze import count_cooccurrences, count_references

query = "diabetes"
grounder = load_grounder("phenotype")
annotated_articles = annotate_abstracts_from_search(query, grounder=grounder, limit=300)

# Analysis
reference_counter = count_references(annotated_articles)
co_occurrence_counter = count_cooccurrences(annotated_articles)

Occurrences

Reference	Name	Count
doid:9351	diabetes mellitus	95
doid:9352	type 2 diabetes mellitus	54
mesh:D013812	treatment	52
doid:4	disease	49
mesh:D012380	Role	31
efo:0001461	control	29
efo:0000246	age	28
mesh:D001244	Association	26
mondo:0021137	not rare	25
efo:0003919	risk factor	24

Co-occurrences

Left Reference	Left Name	Right Reference	Right Name	Count
doid:9351	diabetes mellitus	mesh:D013812	treatment	32
doid:4	disease	doid:9351	diabetes mellitus	31
doid:9351	diabetes mellitus	doid:9352	type 2 diabetes mellitus	21
doid:4	disease	mesh:D013812	treatment	20
doid:9351	diabetes mellitus	mondo:0021137	not rare	18
doid:9351	diabetes mellitus	mesh:D012380	Role	17
doid:9352	type 2 diabetes mellitus	efo:0000246	age	16
doid:9352	type 2 diabetes mellitus	efo:0001461	control	16
doid:9351	diabetes mellitus	efo:0003919	risk factor	16
doid:4	disease	doid:9352	type 2 diabetes mellitus	15

A few things that are immediately obvious:

1. Need some notion of exclude lists in the lexica construction to remove frequently occurring, but not specific entities like "Disease" and "Role"

[codecov]

Codecov Report

Attention: 164 lines in your changes are missing coverage. Please review.

Comparison is base (7b16129) 23.83% compared to head (d965793) 13.17%.

❗ Current head d965793 differs from pull request most recent head 874d926. Consider uploading reports for the commit 874d926 to get more accurate results

Files	Patch %	Lines
src/biolexica/literature/annotate.py	0.00%	53 Missing ⚠️
src/biolexica/literature/retrieve.py	0.00%	46 Missing and 1 partial ⚠️
src/biolexica/literature/search.py	0.00%	24 Missing ⚠️
src/biolexica/literature/__main__.py	0.00%	15 Missing ⚠️
src/biolexica/literature/analyze.py	0.00%	11 Missing ⚠️
src/biolexica/api.py	23.07%	8 Missing and 2 partials ⚠️
src/biolexica/literature/__init__.py	0.00%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
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- Coverage   23.83%   13.17%   -10.67%     
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  Files           6       12        +6     
  Lines         172      334      +162     
  Branches       37       63       +26     
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+ Hits           41       44        +3     
- Misses        129      286      +157     
- Partials        2        4        +2     

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