Configure reference validator to silence unfetchable refs (#57)

Drive down `just validate-references-all` errors from 101 to 62 by
adding a project-level config for linkml-reference-validator and
opportunistically refreshing one cache via the new PMC fallback.

Changes:
- New `conf/reference_validator.yaml` config wired into the
  `validate-references` and `validate-references-all` just targets
  via the validator's `--config` flag:
  - `skip_prefixes: [BIOPROJECT]` so BIOPROJECT accessions like
    PRJNA1272773 stop erroring (the validator's Entrez fetch path
    hits a DTD tag-validation issue on these and there's no
    abstract to validate anyway).
  - `unknown_prefix_severity: WARNING` so the ~35 paywalled DOIs
    that fail both Crossref and DataCite degrade from ERROR to
    WARNING. The references stay in the data; the validator just
    stops failing the run for content it cannot fetch.
- Refresh `references_cache/DOI_10.3389_fmicb.2018.01853.md` via
  the PR #52 PMC fallback chain (DOI -> PMCID PMC6119820 -> JATS
  abstract); recovers 4 "No content available" errors across the
  communities that cite it.

The remaining 62 errors are all "No content available" for caches
that are genuinely paywalled with no OA mirror (older Springer,
Elsevier, IJSEM, etc.) - the validator's hardcoded ERROR severity
on empty cache content can't be relaxed via config, so these would
require either upstream curation changes or a feature ask to the
validator package.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: realmarcin

conf/reference_validator.yaml

@@ -0,0 +1,4 @@
+cache_dir: references_cache
+skip_prefixes:
+  - BIOPROJECT
+unknown_prefix_severity: WARNING

justfile

@@ -25,14 +25,14 @@ validate-all:
 
 # Validate evidence references in a community file
 validate-references FILE:
-    uv run linkml-reference-validator validate data {{FILE}} -s src/communitymech/schema/communitymech.yaml
+    uv run linkml-reference-validator validate data {{FILE}} -s src/communitymech/schema/communitymech.yaml --config conf/reference_validator.yaml
 
 # Validate references in all community files
 validate-references-all:
     #!/usr/bin/env bash
     for file in kb/communities/*.yaml; do
         echo "\\nValidating references in $file..."
-        uv run linkml-reference-validator validate data "$file" -s src/communitymech/schema/communitymech.yaml
+        uv run linkml-reference-validator validate data "$file" -s src/communitymech/schema/communitymech.yaml --config conf/reference_validator.yaml
     done
 
 # Validate ontology terms in a community file

references_cache/DOI_10.3389_fmicb.2018.01853.md

@@ -21,7 +21,7 @@ authors:
 journal: Frontiers in Microbiology
 year: '2018'
 doi: 10.3389/fmicb.2018.01853
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Inoculation of Sinorhizobium saheli YH1 Leads to Reduced Metal Uptake for Leucaena leucocephala Grown in Mine Tailings and Metal-Polluted Soils
@@ -30,3 +30,50 @@ content_type: unavailable
 **DOI:** [10.3389/fmicb.2018.01853](https://doi.org/10.3389/fmicb.2018.01853)
 
 ## Content
+
+1. Front Microbiol. 2018 Aug 27;9:1853. doi: 10.3389/fmicb.2018.01853.
+eCollection  2018.
+
+Inoculation of Sinorhizobium saheli YH1 Leads to Reduced Metal Uptake for 
+Leucaena leucocephala Grown in Mine Tailings and Metal-Polluted Soils.
+
+Kang X(1)(2), Yu X(1), Zhang Y(1), Cui Y(3), Tu W(3), Wang Q(3), Li Y(1), Hu 
+L(1), Gu Y(1), Zhao K(1), Xiang Q(1), Chen Q(1), Ma M(1), Zou L(1), Zhang X(1), 
+Kang J(4).
+
+Author information:
+(1)College of Resources, Sichuan Agricultural University, Chengdu, China.
+(2)Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, 
+United Kingdom.
+(3)Sichuan Provincial Academy of Natural Resource and Sciences, Chengdu, China.
+(4)Sichuan Earthquake Administration, Chengdu, China.
+
+Metalliferous mine tailings have a negative impact on the soil environment near 
+mining areas and render cultivable lands infertile. Phytoremediation involving 
+the synergism of legume and rhizobia provides a useful technique in tackling 
+this issue with cost-effective, environmentally friendly, and easy-to-use 
+features under adverse soil conditions. Leucaena leucocephala has been found to 
+build symbiotic relationships with native rhizobia in the iron-vanadium-titanium 
+oxide (V-Ti magnetite) mine tailing soil. Rhizobia YH1, isolated from the root 
+nodules of L. leucocephala, was classified as Sinorhizobium saheli according to 
+similarity and phylogenetic analyses of 16S rRNA, housekeeping and nitrogen 
+fixation genes. Besides nitrogen fixation, S. saheli YH1 also showed 
+capabilities to produce indole-acetic acid (IAA) (166.77 ± 2.03 mg l-1) and 
+solubilize phosphate (104.41 ± 7.48 mg l-1). Pot culture experiments showed that 
+strain YH1 increased the biomass, plant height and root length of L. 
+leucocephala by 67.2, 39.5 and 27.2% respectively. There was also an average 
+increase in plant N (10.0%), P (112.2%) and K (25.0%) contents compared to 
+inoculation-free control. The inoculation of YH1 not only reduced the uptake of 
+all metals by L. leucocephala in the mine tailings, but also resulted in 
+decreased uptake of Cd by up to 79.9% and Mn by up to 67.6% for plants grown in 
+soils contaminated with Cd/Mn. It was concluded that S. saheli YH1 possessed 
+multiple beneficial effects on L. leucocephala grown in metalliferous soils. Our 
+findings highlight the role of S. saheli YH1 in improving plant health of L. 
+leucocephala by reducing metal uptake by plants grown in heavy metal-polluted 
+soils. We also suggest the idea of using L. leucocephala-S. saheli association 
+for phytoremediation and revegetation of V-Ti mine tailings and soils polluted 
+with Cd or Mn.
+
+DOI: 10.3389/fmicb.2018.01853
+PMCID: PMC6119820
+PMID: 30210458