OpenAlex/Semantic Scholar/Europe PMC fallbacks + snippet fixes (62 -> 43) (#58)

* Add OpenAlex / Semantic Scholar / Europe PMC fallbacks + snippet fixes

Drive `just validate-references-all` errors from 62 to 43 by extending
the literature fetcher's fallback chain past PubMed/PMC and repairing
the snippets that newly-available abstracts surfaced.

Fetcher (src/communitymech/literature.py):
- fetch_openalex_abstract(): reconstruct linear text from OpenAlex's
  abstract_inverted_index (term -> [positions]). Covers older non-OA
  titles (pre-1995 IJSEM, Springer, Elsevier) that Crossref/DataCite
  do not have abstracts for.
- fetch_semantic_scholar_abstract(): GET /graph/v1/paper/DOI:<doi>
  ?fields=abstract. Sometimes carries recent Elsevier abstracts that
  Crossref hides.
- fetch_europepmc_abstract(): EPMC core search by DOI. Broader life-
  science coverage than US PMC; mirrors abstracts for some Springer/
  Wiley records.
- fetch_paper() fallback chain extended to:
  CrossRef -> PMID/PubMed -> PMCID/PMC -> OpenAlex
            -> Semantic Scholar -> Europe PMC

Cache refresh (recovers 17 ERROR rows across 6 communities):
- DOI_10.1099_00207713-36-2-197 (Wichlacz 1986 Acidiphilium taxonomy,
  OpenAlex)
- DOI_10.1016_j.hydromet.2020.105484 (NEMO Terrafame bioleaching,
  OpenAlex; cited 10x)
- DOI_10.1186_s12302-025-01103-y (OpenAlex)
- DOI_10.1134_S0026261716060059 (OpenAlex)
- DOI_10.1007_s13213-019-01453-y (OpenAlex)
- DOI_10.1007_s11274-009-0047-x (Europe PMC)
- DOI_10.1016_j.cej.2020.125159 -> 10.1016/j.cej.2020.124801 (typo
  in original DOI; the wrong DOI points to an OLED chemistry paper.
  Correct DOI located via Crossref title search; cache written via
  Semantic Scholar for the right paper.)

Snippet repairs on the 7 newly-surfaced "Text part not found" errors:
- AMD_Acidophile_Heterotroph_Network: three snippets paraphrased
  away from the 1986 abstract. The paper describes A. rubrum/
  angustum/facilis, not A. multivorum, and does not quote pH 2.5-3.5
  or 30-35 deg C optima. Replaced with verbatim substrings;
  downgraded to PARTIAL/WRONG_STATEMENT as appropriate.
- Chromium_Sulfur_Reduction_Enrichment: DOI typo fixed and snippet
  rewritten; second snippet downgraded to PARTIAL where review
  abstract supports the bioremediation method but not the specific
  numeric figure.
- Industrial_Bioreactor_Consortium / Rammelsberg_Cobalt_Nickel_
  Tailings: replaced paraphrases with verbatim substrings.

Remaining 43 "No content available" errors all map to papers
genuinely not abstracted anywhere we can query (Springer book
chapters, paywalled older PNAS/AEM/femsec without PubMed records,
recent 2024-2025 Elsevier titles that none of CrossRef/OpenAlex/
Semantic Scholar/Europe PMC has indexed yet).

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

* Address Copilot review on PR #58

- Rammelsberg_Cobalt_Nickel_Tailings snippet: replace the
  `..`-split snippet with the full verbatim run from the abstract:
  "Cobalt dissolution kinetics were highly improved by the bacterial
  activity, whatever the consortium. This is consistent with the
  presence of Co in the pyrite in the secondary ore". One contiguous
  substring is cleaner than the double-period splitter trick when
  the full phrase is available verbatim.
- Industrial_Bioreactor_Consortium snippet: replace the pH/gene-
  expression methodology line with the abstract's verbatim taxonomic
  finding that "Sulfobacillus thermosulfidooxidans and
  Acidithiobacillus caldus were the dominant species during the
  early stage". That directly supports A. caldus' early-stage
  sulfur-oxidizing role in the consortium, which is what the
  evidence is being used to back.
- references_cache/DOI_10.1016_j.cej.2020.124801.md: replace the
  `Anonymous` author stub with the actual Crossref author list
  (Zhao, Sun, Li, Yu, Jin, Wang, Liang, Zhang).
- src/communitymech/literature.py: add on-disk caching to
  fetch_openalex_abstract, fetch_semantic_scholar_abstract, and
  fetch_europepmc_abstract via a shared `_abstract_cache_path`
  helper. Mirrors the cache pattern already used by
  fetch_pubmed_abstract and fetch_pmc_abstract, so repeated runs
  (validator, refresh scripts, smoke tests) do not re-hit the
  rate-limited external APIs.

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

---------

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

Author: realmarcin

kb/communities/AMD_Acidophile_Heterotroph_Network.yaml

@@ -59,11 +59,13 @@ taxonomy:
   abundance_value: Major component of heterotrophic populations in pH 2.5-3.5 AMD
   evidence:
   - reference: doi:10.1099/00207713-36-2-197
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VIVO
-    snippet: Acidiphilium multivorum sp. nov., an acidophilic chemoorganotrophic bacterium from pyritic
-      acid mine drainage
-    explanation: Establishes isolation from AMD and heterotrophic metabolism
+    snippet: Acidophilic heterotrophic bacteria recovered from samples of water and sediment
+      collected from acidic mine drainage streams
+    explanation: Supports isolation of acidophilic heterotrophic Acidiphilium from AMD;
+      the cited paper describes A. rubrum/angustum/facilis (not multivorum), so genus-level
+      support for the AMD-origin claim is partial.
   - reference: PMID:10427060
     supports: SUPPORT
     evidence_source: IN_VITRO
@@ -654,10 +656,11 @@ environmental_factors:
       capable of utilizing organic matter have been isolated from natural and man-made environments
     explanation: Documents pH preference of heterotrophic acidophiles
   - reference: doi:10.1099/00207713-36-2-197
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: IN_VITRO
-    snippet: Acidiphilium species isolated from acidic coal mine drainage grow optimally at pH 2.5-3.5
-    explanation: Establishes optimal pH range for Acidiphilium
+    snippet: unable to grow at or above pH 6.0
+    explanation: Establishes the upper pH boundary for these AMD Acidiphilium isolates;
+      the abstract does not quote the 2.5-3.5 optimum specifically, so support is partial.
 - name: Dissolved Organic Carbon
   value: Variable, 10-500 mg/L
   unit: mg/L DOC
@@ -731,10 +734,13 @@ environmental_factors:
     '
   evidence:
   - reference: doi:10.1099/00207713-36-2-197
-    supports: SUPPORT
+    supports: WRONG_STATEMENT
     evidence_source: IN_VITRO
-    snippet: Acidiphilium species grow optimally at 30-35°C
-    explanation: Documents mesophilic temperature preference
+    snippet: All 37 bacterial strains examined were rod shaped, motile, gram negative,
+      and strictly aerobic
+    explanation: The 1986 Acidiphilium taxonomy paper does not report a temperature
+      optimum; the 30-35°C figure is not supported by this reference. Marked as
+      WRONG_STATEMENT - reference is misattributed for this specific claim.
 - name: Metal Concentrations
   value: 'Fe: 0.5-5 g/L; Zn: 100-1000 mg/L; Cu: 50-500 mg/L'
   unit: g/L or mg/L

kb/communities/Chromium_Sulfur_Reduction_Enrichment.yaml

@@ -327,12 +327,15 @@ ecological_interactions:
       proposed to drive chromate removal from contaminated water, little is known for microbial chromate
       reduction coupled to elemental sulfur (S(0)) or zerovalent iron (Fe(0)) oxidation
     explanation: Demonstrates coupling of Cr reduction to sulfur oxidation pathways
-  - reference: doi:10.1016/j.cej.2020.125159
+  - reference: doi:10.1016/j.cej.2020.124801
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: Driving microbial sulfur cycle for phenol degradation coupled with Cr(VI) reduction via Fe(III)/Fe(II)
-      transformation
-    explanation: Establishes sulfur cycling coupled to chromium reduction mechanisms
+    snippet: Microbial sulphur cycle is of great importance to anaerobic degradation of
+      organic pollutants coupled with metal reduction
+    explanation: Establishes sulfur cycling coupled to chromium reduction mechanisms.
+      (The previous DOI 10.1016/j.cej.2020.125159 was a typo - that DOI points to an
+      unrelated OLED chemistry paper; the correct DOI for the cited Cr(VI)/sulfur work
+      is 10.1016/j.cej.2020.124801.)
 - name: Chromium Immobilization via Cr(III) Precipitation
   description: 'Biogenic Cr(III) produced by microbial Cr(VI) reduction undergoes rapid precipitation
     as chromium hydroxide and chromium-organic complexes, effectively immobilizing chromium in the solid
@@ -485,11 +488,14 @@ environmental_factors:
     '
   evidence:
   - reference: doi:10.1186/s12302-025-01103-y
-    supports: SUPPORT
+    supports: PARTIAL
     evidence_source: REVIEW
-    snippet: Chromium contamination in industrial sites reaches hundreds to thousands mg/kg requiring
-      bacterial bioremediation
-    explanation: Documents chromium contamination levels in industrial environments
+    snippet: Bacterial bioremediation is an eco-friendly and cost-effective method for
+      treating metal-contaminated industrial effluent
+    explanation: Review establishes bacterial bioremediation as the standard approach
+      for metal-contaminated industrial effluent. Specific "hundreds to thousands mg/kg"
+      chromium figures are not in the abstract, so support for that quantitative claim
+      is partial.
 - name: Dissolved Cr(VI) Concentration
   value: 50-200
   unit: mg/L

kb/communities/Industrial_Bioreactor_Consortium.yaml

@@ -451,9 +451,11 @@ ecological_interactions:
   - reference: doi:10.1007/s13213-019-01453-y
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: Expression of key sulfur oxidation genes during bioleaching of chalcopyrite under thermophilic
-      conditions
-    explanation: Demonstrates thermophilic sulfur oxidation activity
+    snippet: Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the
+      dominant species during the early stage
+    explanation: Establishes A. caldus as a dominant early-stage species in moderately
+      thermophilic chalcopyrite bioleaching, supporting its role as a sulfur-oxidizing
+      acidophile in the reactor consortium.
 - name: Mid-Stage Mixotrophic Iron Oxidation
   description: 'During mid-stage reactor operation (days 10-15), Sulfobacillus benefaciens becomes predominant,
     reaching 62-66% of consortium composition. This facultatively autotrophic organism bridges the ecological

kb/communities/Rammelsberg_Cobalt_Nickel_Tailings.yaml

@@ -240,9 +240,11 @@ ecological_interactions:
   - reference: doi:10.1016/j.hydromet.2020.105484
     supports: SUPPORT
     evidence_source: IN_VITRO
-    snippet: Mineralogical analysis showed that cobalt occurred on the surface of framboidal pyrite and
-      was mainly leached by microbial attack
-    explanation: Establishes cobalt association with pyrite and bioleaching mechanism
+    snippet: Cobalt dissolution kinetics were highly improved by the bacterial activity,
+      whatever the consortium. This is consistent with the presence of Co in the pyrite
+      in the secondary ore
+    explanation: Establishes cobalt association with pyrite and the role of bacterial
+      activity in cobalt leaching from the secondary ore.
 - name: Sulfur Oxidation and Acid Generation
   description: 'Acidithiobacillus thiooxidans oxidizes elemental sulfur (S⁰) that accumulates as a passivation
     layer on sulfide mineral surfaces during ferric iron attack. The oxidation reaction (S²⁻ + 2H₂O +

references_cache/DOI_10.1007_s11274-009-0047-x.md

@@ -8,7 +8,7 @@ authors:
 journal: World Journal of Microbiology and Biotechnology
 year: '2009'
 doi: 10.1007/s11274-009-0047-x
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Removal of toxic chromate using free and immobilized Cr(VI)-reducing bacterial cells of Intrasporangium sp. Q5-1
@@ -17,3 +17,5 @@ content_type: unavailable
 **DOI:** [10.1007/s11274-009-0047-x](https://doi.org/10.1007/s11274-009-0047-x)
 
 ## Content
+
+Chromate-reducing microorganisms with the ability of reducing toxic chromate [Cr(VI)] into insoluble trivalent chromium [Cr(III)] are very useful in treatment of Cr(VI)-contaminated water. In this study, a novel chromate-reducing bacterium was isolated from Mn/Cr-contaminated soil. Based on morphological, physiological/biochemical characteristics and 16S rRNA gene sequence analyses, this strain was identified as Intrasporangium sp. strain Q5-1. This bacterium has high Cr(VI) resistance with a MIC of 17 mmol l⁻¹ and is able to reduce Cr(VI) aerobically. The best condition of Cr(VI) reduction for Q5-1 is pH 8.0 at 37°C. Strain Q5-1 is also able to reduce Cr(VI) in resting (non-growth) conditions using a variety of carbon sources as well as in the absence of a carbon source. Acetate (1 mmol l⁻¹) is the most efficient carbon source for stimulating Cr(VI) reduction. In order to apply strain Q5-1 to remove Cr(VI) from wastewater, the bacterial cells were immobilized with different matrices. Q5-1 cells embedded with compounding beads containing 4% PVA, 3% sodium alginate, 1.5% active carbon and 3% diatomite showed a similar Cr(VI) reduction rates to that of free cells. In addition, the immobilized Q5-1 cells have the advantages over free cells in being more stable, easier to re-use and minimal clogging in continuous systems. This study provides potential applications of a novel immobilized chromate-reducing bacterium for Cr(VI) bioremediation.

references_cache/DOI_10.1007_s13213-019-01453-y.md

@@ -11,7 +11,7 @@ authors:
 journal: Annals of Microbiology
 year: '2019'
 doi: 10.1007/s13213-019-01453-y
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Effects of pH value on the expression of key iron/sulfur oxidation genes during bioleaching of chalcopyrite on thermophilic condition
@@ -20,3 +20,5 @@ content_type: unavailable
 **DOI:** [10.1007/s13213-019-01453-y](https://doi.org/10.1007/s13213-019-01453-y)
 
 ## Content
+
+Physicochemical factors such pH value would affect the microbial metabolism during chalcopyrite bioleaching. To this end, the effects of pH on the expression of critical functional genes during bioleaching were evaluated. A mixed culture of moderate thermophiles was used for chalcopyrite bioleaching at initial pH values of 1.0, 2.0, and 3.0, and bioleaching processes were monitored via measuring the physicochemical parameters. Quantitative real-time PCR assay was used to monitor the dynamics of microbial community structures and the expression of critical iron/sulfur oxidation genes (4Fe-4S ferredoxin and sulfate adenylyltransferase genes, respectively). Redundancy analysis and calculation of correlation coefficients were used to reveal linkages between gene expression and various physicochemical factors. The leaching processes at initial pH of 1.0 and 3.0 were prolonged compared with that at initial pH of 2.0. It was shown that Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus were the dominant species during the early stage in free and attached cells, respectively, while Ferroplasma thermophilum became predominant in the later phase. The gene expression in Sulfobacillus thermosulfidooxidans and Ferroplasma thermophilum was greatly affected by pH values. On the other hand, the relationship between pH and gene expression in Acidithiobacillus caldus was not significant. The study unraveled the importance of pH value on chalcopyrite bioleaching, and pH selectively influenced the expression of key functional genes of some specific species.

references_cache/DOI_10.1016_j.cej.2020.124801.md

@@ -0,0 +1,24 @@
+---
+reference_id: DOI:10.1016/j.cej.2020.124801
+title: "Driving microbial sulfur cycle for phenol degradation coupled with Cr(VI) reduction via Fe(III)/Fe(II) transformation"
+authors:
+- Zhiqiang Zhao
+- Cheng Sun
+- Yang Li
+- Qilin Yu
+- Zhen Jin
+- Mingwei Wang
+- Lianfu Liang
+- Yaobin Zhang
+journal: Chemical Engineering Journal
+year: '2020'
+doi: 10.1016/j.cej.2020.124801
+content_type: abstract_only
+---
+
+# Driving microbial sulfur cycle for phenol degradation coupled with Cr(VI) reduction via Fe(III)/Fe(II) transformation
+**DOI:** [10.1016/j.cej.2020.124801](https://doi.org/10.1016/j.cej.2020.124801)
+
+## Content
+
+Abstract Microbial sulphur cycle is of great importance to anaerobic degradation of organic pollutants coupled with metal reduction, which however is usually limited by the poor oxidation of the elemental sulphur to sulphate, due to the lack of chemolithotrophic sulphur-oxidizing bacteria. The study presented here utilized magnetite as an Fe(III) source to enrich the chemolithotrophic sulphur-oxidizing bacteria to proceed the oxidation of the elemental sulphur, which further achieved the whole sulphur cycle. The results showed that, under the low-concentration sulphate conditions, the effluent concentration of both Cr(VI) (18.0 mg/L vs 187.7 mg/L) and phenol (354.2 mgCOD/L vs 1256.0 mgCOD/L) in the reactor with magnetite was significantly lower than that without magnetite. Energy-dispersive X-ray (EDX) analysis showed that the content of sulphur in the aggregates without magnetite was lower than that with magnetite (4.49% vs 6.85%). Conversely, with magnetite, the special enrichments, Thiobacillus species, proceeded the oxidation of the elemental sulphur to sulphate, lowering the loss of sulphur. Further analysis by X-ray Diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) observed the disappearance of the crystalline structure in magnetite as well as the loss of iron via the dissimilatory Fe(III) reduction in the aggregates. However, under the sulphate-reducing conditions, the evident peaks of both Fe2O3 and FeO were detected in the aggregates. Considered that the re-oxidation of the reduced Cr(III) might occur in the aggregates without magnetite, the generated Fe(II) might react with the slight dissolved oxygen (DO) to reduce the re-oxidation of the reduced Cr(III), which further achieved the transformation of Fe(III)/Fe(II).

references_cache/DOI_10.1016_j.cej.2020.125159.md

@@ -8,7 +8,7 @@ authors:
 journal: Chemical Engineering Journal
 year: '2020'
 doi: 10.1016/j.cej.2020.125159
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Concentration quenching resistant donor-acceptor molecular structure for high efficiency and long lifetime thermally activated delayed fluorescent organic light-emitting diodes via suppressed non-radiative channel
@@ -17,3 +17,5 @@ content_type: unavailable
 **DOI:** [10.1016/j.cej.2020.125159](https://doi.org/10.1016/j.cej.2020.125159)
 
 ## Content
+
+Abstract A molecular design having t-butyl groups surrounding a donor-acceptor type core structure was developed as an approach to obtain high external quantum efficiency by suppressing concentration quenching effect caused by strong intermolecular interaction. The donor-acceptor type core structure was surrounded by six t-butyl groups to separate the donor-acceptor core structure between molecules. A heptazine acceptor and a diphenylamine donor based thermally activated delayed fluorescent emitter protected by the multiple t-butyl units achieved maximum external quantum efficiency of 32.6% at 1% doping concentration and 23.0% even at a high doping concentration of 20% by reducing concentration quenching effect. Furthermore, the lifetime of the thermally activated delayed fluorescent devices was also improved relative to that of the previous emitter with the same acceptor. The external quantum efficiency and device lifetime are better than any other results reported in the orange TADF OLEDs.

references_cache/DOI_10.1016_j.hydromet.2020.105484.md

@@ -11,7 +11,7 @@ authors:
 journal: Hydrometallurgy
 year: '2020'
 doi: 10.1016/j.hydromet.2020.105484
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Bioleaching to reprocess sulfidic polymetallic primary mining residues: Determination of metal leaching mechanisms
@@ -20,3 +20,5 @@ content_type: unavailable
 **DOI:** [10.1016/j.hydromet.2020.105484](https://doi.org/10.1016/j.hydromet.2020.105484)
 
 ## Content
+
+The mining of non-ferrous metals produces the largest volume of metal-containing, extractive waste in Europe, and about 29% of all the waste produced in the EU-28. In the framework of the European project NEMO (Near-zero-waste recycling of low-grade sulfidic mining waste for critical-metal, mineral and construction raw-material production in a circular economy), new ways to valorize sulfidic tailings are being developed through the recovery of valuable metals and critical raw materials and the transformation of the residual in clean mineral fraction to be used for the mass production of cement, concrete and construction products. The first step of the NEMO concept consists of removing the sulfides remaining from primary bioleaching and extracting the metals in the residual material (known as ‘secondary ore’) using either enhanced bioleaching or an alkaline autoclave conversion processes. This paper focuses on one of the project case studies, the secondary ore, obtained from an operating heap leaching plant (Terrafame, Finland). This material still contains several sulfide minerals (pyrrhotite, pyrite, sphalerite, pentlandite, violarite, chalcopyrite) and significant amounts of metals (Zn, Ni, Cu, Co, rare earth elements). The study aimed to characterize the mineralogy of the secondary ore and perform bioleaching in 2 L-stirred tank reactors, with three microbial cultures growing at 42, 48 and 55 °C. These results were compared to abiotic experiments, performed under the same conditions. Nickel was released very quickly, suggesting that part of Ni dissolved in the primary heap was re-precipitated and remained in the secondary ore. By contrast, Cu dissolution was much slower but the kinetics were substantially improved when the temperature was increased to 55 °C. Cobalt dissolution kinetics were highly improved by the bacterial activity, whatever the consortium. This is consistent with the presence of Co in the pyrite in the secondary ore.

references_cache/DOI_10.1099_00207713-36-2-197.md

@@ -8,7 +8,7 @@ authors:
 journal: International Journal of Systematic Bacteriology
 year: '1986'
 doi: 10.1099/00207713-36-2-197
-content_type: unavailable
+content_type: abstract_only
 ---
 
 # Acidiphilium angustum sp. nov., Acidiphilium facilis sp. nov., and Acidiphilium rubrum sp. nov.: Acidophilic Heterotrophic Bacteria Isolated from Acidic Coal Mine Drainage
@@ -17,3 +17,5 @@ content_type: unavailable
 **DOI:** [10.1099/00207713-36-2-197](https://doi.org/10.1099/00207713-36-2-197)
 
 ## Content
+
+Acidophilic heterotrophic bacteria recovered from samples of water and sediment collected from acidic mine drainage streams were compared nutritionally, genetically, and morphologically. All 37 bacterial strains examined were rod shaped, motile, gram negative, and strictly aerobic, utilized citric acid and Tween 80 as sole carbon sources, and were unable to grow at or above pH 6.0. The ultrastructure of representative strains was not markedly different from that of gram-negative bacteria. Differences among the strains were evident in cell size (4.2 by 0.6 to 1.2 by 0.6 p.m), pigmentation (when present), and nutritional faculties (the carbon sources suitable for growth of individual strains ranged from 8 to 20 of the 32 compounds tested). The guanine-plus-cytosine base composition of eight typical strains ranged from 63 to 68 mol%. All of the strains exhibited primary characteristics of the recently described genus Acidiphilium; however, important differences between our strains and the type species Acidiphilium cryptum suggested that new Acidiphilium species should be described. No significant deoxyribonucleic acid-deoxyribonucleic acid homology was found between five acidophilic heterotrophic strains and A. cryptum. Furthermore, no significant deoxyribonucleic acid-deoxyribonucleic acid homology was evident between the acidophilic heterotrophs and six Thiobacillus species. The bacteria which we studied could be divided into three groups based on genetic and nutritional characteristics. We propose the following three new species: Acidiphilium rubrum (type strain, strain OP [= ATCC 35905]), Acidiphilium angustum (type strain, strain KLB [= ATCC 35903]), and Acidiphilium facilis (type strain, strain PW2 [= ATCC 35904]).