diff --git a/docs/troubleshooting.md b/docs/troubleshooting.md
index 15d2bec..8fbf1e3 100644
--- a/docs/troubleshooting.md
+++ b/docs/troubleshooting.md
@@ -785,3 +785,51 @@ Run through this checklist when encountering issues:
 - [CLI Reference](reference/cli.md) - Complete command documentation
 - [How to Repair Validation Errors](how-to/repair-validation-errors.md) - Fixing common issues
 - [GitHub Issues](https://github.com/linkml/linkml-reference-validator/issues) - Report bugs
+
+### JATS tables and XML cache refresh
+
+JATS/PMC XML extraction appends pipe-delimited tables after the existing body
+paragraphs. Tables are found throughout the document, including `floats-group`
+when there is no body. Labels and captions form headings; table paragraphs do
+not also appear as body prose. Other existing body paragraphs, such as table
+attribution or alternative descriptions, are retained. Abstract extraction remains the source's job.
+Restricted body notices are checked before any tables are appended.
+
+Each actual table is rendered once, including tables inside nested wrappers.
+Nested tables without their own wrapper use a generic `Nested table` heading.
+Inline text and symbols are retained, block/line breaks become spaces, and
+literal backslashes and pipes in cells are escaped. Rows preserve source cell
+order, including empty cells. A span is printed as `[rowspan=2]` or
+`[colspan=2]` on its source cell: values are not copied into other rows or
+columns. These are quotable source rows, not a reconstructed rectangular grid;
+interpret spanned rows using the original table. Images and non-HTML table
+encodings are not transcribed, but their labels/captions are retained.
+As in existing body extraction, superscript/subscript text is flattened:
+`10<sup>9</sup>` becomes `109`, not exponent notation. Consult the original
+for numeric interpretation; superscript styling is not preserved.
+
+The first **200 source rows per table**, including header and empty rows, are
+kept. Larger tables end with `[Table truncated after 200 rows.]`; later rows
+cannot be validated from this cache. Table footnotes in `table-wrap-foot` are retained once in document order,
+including notes in `floats-group`. The cap is per table, not per document.
+
+`full_text_xml` entries now carry `xml_extraction_version: 1`, independently of
+`extractor_version` and `html_full_text_version`. Missing/older XML stamps cause
+refresh on the next validation fetch; current PDF and HTML entries need no
+refresh for this change. Fresh source/provider XML is stamped after acquisition.
+Inventory and metadata-only rewrites preserve the original XML stamp, including
+future versions, and never certify old text. If refresh is unavailable, legacy
+XML remains available with the existing stale-cache warning and is not rewritten;
+it may still lack table rows. A later process retries the refresh. Existing
+stale HTML rejection remains unchanged.
+
+A successful source refresh that returns only an abstract can replace the old
+full text if no provider supplies a body. This is existing refresh behavior;
+the stale fallback applies when the source returns no record, not when it
+returns an abstract-only record. Keep a backup if retaining older full text is
+necessary.
+
+This pass targets JATS `table-wrap` content and searches the whole document;
+tables and notes inside embedded `sub-article` or `response` elements are
+excluded so reviewer/reply findings are not attributed to the main paper. Bare tables
+without a `table-wrap` remain outside this JATS extraction pass.
diff --git a/src/linkml_reference_validator/etl/extract/__init__.py b/src/linkml_reference_validator/etl/extract/__init__.py
index 41bb10d..290deab 100644
--- a/src/linkml_reference_validator/etl/extract/__init__.py
+++ b/src/linkml_reference_validator/etl/extract/__init__.py
@@ -5,7 +5,10 @@
 When a change means previously cached text is *wrong* rather than merely older,
 bump ``EXTRACTOR_CACHE_VERSION`` in
 :mod:`linkml_reference_validator.etl.reference_fetcher` so existing entries are
-re-fetched instead of keeping the old output forever.
+re-fetched instead of keeping the old output forever. For changes confined to
+XML table extraction, bump ``XML_EXTRACTION_CACHE_VERSION`` instead; HTML
+acceptance has its own ``HTML_FULL_TEXT_CACHE_VERSION``. These format-specific
+stamps avoid refreshing unchanged formats.
 """
 
 from linkml_reference_validator.etl.extract.base import Extractor, ExtractorRegistry
diff --git a/src/linkml_reference_validator/etl/extract/xml.py b/src/linkml_reference_validator/etl/extract/xml.py
index 42c2719..463fa25 100644
--- a/src/linkml_reference_validator/etl/extract/xml.py
+++ b/src/linkml_reference_validator/etl/extract/xml.py
@@ -2,13 +2,14 @@
 
 Changing what this yields for the same input may make already-cached text wrong
 rather than merely older; see :mod:`linkml_reference_validator.etl.extract` for
-when to bump ``EXTRACTOR_CACHE_VERSION``.
+when to bump cache versions. Table changes use ``XML_EXTRACTION_CACHE_VERSION``
+so PDF and HTML entries remain current.
 """
 
 import logging
 from typing import Optional, Union
 
-from bs4 import BeautifulSoup  # type: ignore
+from bs4 import BeautifulSoup, CData, NavigableString, Tag  # type: ignore
 
 from linkml_reference_validator.etl.extract.base import Extractor, ExtractorRegistry
 
@@ -83,18 +84,117 @@ def is_stub_notice(text: str) -> bool:
     return any(phrase in lowered for phrase in STUB_NOTICE_PHRASES)
 
 
+#: Bound cached table evidence; headers count and truncation is always explicit.
+MAX_TABLE_ROWS = 200
+
+
+def _table_text(node: Tag) -> str:
+    """Keep inline text contiguous, separating blocks and excluding nested tables."""
+
+    def walk(tag: Tag) -> str:
+        """Render descendants without mutating the parsed document."""
+        parts = []
+        for child in tag.children:
+            if type(child) in (NavigableString, CData):
+                parts.append(str(child))
+            elif isinstance(child, Tag) and child.name not in {"table", "table-wrap"}:
+                value = walk(child)
+                if child.name in {"p", "break", "br", "list-item", "title"}:
+                    value = " " + value + " "
+                parts.append(value)
+        return "".join(parts)
+
+    return " ".join(walk(node).split())
+
+
+def _table_heading(wrap: Tag) -> str:
+    """Read only the label/caption owned by this wrapper, not nested wrappers."""
+    parts = []
+    for name in ("label", "caption"):
+        node = next(
+            (n for n in wrap.find_all(name) if n.find_parent("table-wrap") is wrap),
+            None,
+        )
+        if node is not None:
+            parts.append(_table_text(node))
+    return " ".join(part for part in parts if part)
+
+
+def _tables_as_text(soup: BeautifulSoup) -> list[str]:
+    """Render each table once in document order, using source cells, not a grid.
+
+    Row/column spans are explicit annotations; values are never replicated or
+    assigned to inferred columns. Header rows count toward the 200-row limit.
+    """
+    sections = []
+    for table in soup.find_all(["table-wrap", "table", "table-wrap-foot"]):
+        if table.find_parent(["sub-article", "response"]):
+            continue
+        if table.name == "table-wrap":
+            heading = _table_heading(table)
+            if heading:
+                sections.append("## " + heading)
+            continue
+        wrap = table.find_parent("table-wrap")
+        if wrap is None:
+            # This pass targets JATS tables, not arbitrary XML layout tables.
+            continue
+        if table.name == "table-wrap-foot":
+            note = _table_text(table)
+            if note:
+                sections.append(note)
+            continue
+        # Named wrapper headings were emitted at their own document position.
+        heading = "" if _table_heading(wrap) else "Table"
+        if table.find_parent(["table", "table-wrap"]) is not wrap:
+            heading = "Nested table"
+        rows = [
+            row for row in table.find_all("tr") if row.find_parent("table") is table
+        ]
+        rendered = []
+        for row in rows[:MAX_TABLE_ROWS]:
+            cells = []
+            for cell in row.find_all(["th", "td"]):
+                if (
+                    cell.find_parent("tr") is not row
+                    or cell.find_parent("table") is not table
+                ):
+                    continue
+                value = _table_text(cell).replace("\\", "\\\\").replace("|", "\\|")
+                for span in ("rowspan", "colspan"):
+                    if cell.has_attr(span) and str(cell[span]) != "1":
+                        value += f" [{span}={cell[span]}]"
+                cells.append(value)
+            if cells:
+                rendered.append("| " + " | ".join(cells) + " |")
+        if len(rows) > MAX_TABLE_ROWS:
+            rendered.append(f"[Table truncated after {MAX_TABLE_ROWS} rows.]")
+        if rendered:
+            sections.append(
+                ("## " + heading + "\n\n" if heading else "") + "\n".join(rendered)
+            )
+    return sections
+
+
 @ExtractorRegistry.register
 class XMLExtractor(Extractor):
     """Extract body text from JATS/PMC article XML.
 
-    Returns the concatenated text of paragraphs within the article ``<body>``.
-    Returns None when there is no body content, and when the body holds one of
+    Returns main-article body paragraphs followed by labeled tables and notes,
+    including floats-group content. Sub-article and response content is excluded.
+    Table cells retain inline text and explicitly annotate spans; the first 200
+    source rows per table are retained, with a notice when rows are omitted.
+    Returns None when neither body paragraphs nor table content exists, and when
+    the body holds one of
     PMC's placeholder notices instead of the article itself.
 
     Examples:
         >>> xml = b"<article><body><p>Hello body.</p></body></article>"
         >>> XMLExtractor().extract(xml)
         'Hello body.'
+        >>> table = "<article><table-wrap><table><tr><td>Yes</td></tr></table></table-wrap></article>"
+        >>> XMLExtractor().extract(table)
+        '## Table\\n\\n| Yes |'
         >>> stub = b"<article><body><p>Text cannot be obtained from PMC.</p></body></article>"
         >>> XMLExtractor().extract(stub) is None
         True
@@ -112,17 +212,28 @@ def extract(
         # re-encoding str here would leave that declaration contradicting the
         # bytes. The parser gets both cases right on its own.
         soup = BeautifulSoup(data, "xml")
-        body = soup.find("body")
-        if not body:
-            return None
-
-        paragraphs = body.find_all("p")
-        if not paragraphs:
-            return None
-
-        text = "\n\n".join(p.get_text() for p in paragraphs if p.get_text().strip())
-        if not text.strip():
-            return None
+        body = next(
+            (
+                node
+                for node in soup.find_all("body")
+                if not node.find_parent(["sub-article", "response"])
+            ),
+            None,
+        )
+        paragraphs = (
+            [
+                p
+                for p in body.find_all("p")
+                if not p.find_parent(["sub-article", "response"])
+            ]
+            if body
+            else []
+        )
+        text = "\n\n".join(
+            p.get_text()
+            for p in paragraphs
+            if not p.find_parent("table-wrap") and p.get_text().strip()
+        )
 
         # Judged on the extracted body, not the raw markup: a citation title or
         # a methods sentence elsewhere in the document says nothing about
@@ -137,4 +248,17 @@ def extract(
             )
             return None
 
-        return text
+        # Keep existing attribution/alternative prose that the renderer does not
+        # emit. Table content must not inflate the stub check above.
+        text = "\n\n".join(
+            p.get_text()
+            for p in paragraphs
+            if p.get_text().strip()
+            and not (
+                p.find_parent("table-wrap")
+                and p.find_parent(["label", "caption", "table", "table-wrap-foot"])
+            )
+        )
+        return (
+            "\n\n".join(part for part in [text, *_tables_as_text(soup)] if part) or None
+        )
diff --git a/src/linkml_reference_validator/etl/reference_fetcher.py b/src/linkml_reference_validator/etl/reference_fetcher.py
index a68a66e..68ec64a 100644
--- a/src/linkml_reference_validator/etl/reference_fetcher.py
+++ b/src/linkml_reference_validator/etl/reference_fetcher.py
@@ -64,6 +64,9 @@
 #: PMC or a configured text provider is trusted under FullTextLocation's contract.
 HTML_FULL_TEXT_CACHE_VERSION = 1
 
+#: XML table extraction changes only XML caches, independent of HTML acceptance.
+XML_EXTRACTION_CACHE_VERSION = 1
+
 #: A cache file's frontmatter delimiter: a line that is exactly ``---``.
 #: Splitting on the bare string instead lets any *value* containing ``---`` - a
 #: URL reference_id, a title - truncate the block, which loses every field after
@@ -184,6 +187,11 @@ def fetch(
                 content.metadata or {}, html_full_text_version=HTML_FULL_TEXT_CACHE_VERSION
             )
 
+        if content and content.content_type == "full_text_xml":
+            content.metadata = dict(
+                content.metadata or {}, xml_extraction_version=XML_EXTRACTION_CACHE_VERSION
+            )
+
         if content and self.config.fetch_full_text and self.needs_full_text(content):
             content = self._enrich_with_full_text(content)
 
@@ -403,6 +411,10 @@ def _apply_full_text_location(
             content.metadata = dict(
                 content.metadata or {}, html_full_text_version=HTML_FULL_TEXT_CACHE_VERSION
             )
+        if fmt == "xml":
+            content.metadata = dict(
+                content.metadata or {}, xml_extraction_version=XML_EXTRACTION_CACHE_VERSION
+            )
         content.full_text_provider = location.provider or provider_name
         # Non-public endpoints are not durable provenance and may contain
         # session-specific access information.
@@ -711,6 +723,10 @@ def _save_to_disk(
         html_version = (reference.metadata or {}).get("html_full_text_version")
         if reference.content_type == "full_text_html" and isinstance(html_version, int):
             lines.append(f"html_full_text_version: {html_version}")
+        # YAML booleans are not extraction versions, despite bool subclassing int.
+        xml_version = (reference.metadata or {}).get("xml_extraction_version")
+        if reference.content_type == "full_text_xml" and type(xml_version) is int:
+            lines.append(f"xml_extraction_version: {xml_version}")
         if reference.title:
             lines.append(f"title: {self._quote_yaml_value(reference.title)}")
         if reference.authors:
@@ -976,7 +992,7 @@ def _split_frontmatter(content_text: str) -> Optional[tuple[str, str]]:
 
     @classmethod
     def _is_stale_cache_entry(cls, content_text: str) -> bool:
-        """Report whether extraction or HTML full-text acceptance needs refreshing.
+        """Report whether extraction or format-specific full-text processing needs refreshing.
 
         Deliberately not applied by :meth:`iter_cached_references`: export and
         enrichment walk the cache as a record of what was fetched, and dropping
@@ -1017,6 +1033,11 @@ def _is_stale_cache_entry(cls, content_text: str) -> bool:
             ):
                 return True
 
+        if isinstance(metadata, dict) and metadata.get("content_type") == "full_text_xml":
+            xml_version = metadata.get("xml_extraction_version")
+            if type(xml_version) is not int or xml_version < XML_EXTRACTION_CACHE_VERSION:
+                return True
+
         # A newer stamp is not stale: an older tool reading a cache written by a
         # newer one should leave it alone rather than re-fetch it on every run.
         return False
@@ -1056,6 +1077,8 @@ def _load_markdown_format(
         )
 
         metadata: dict = {}
+        if "xml_extraction_version" in frontmatter:
+            metadata["xml_extraction_version"] = frontmatter["xml_extraction_version"]
         if "html_full_text_version" in frontmatter:
             metadata["html_full_text_version"] = frontmatter["html_full_text_version"]
         if "extra_fields_captured" in frontmatter:
diff --git a/tests/fixtures/jats/PMC5593426.xml b/tests/fixtures/jats/PMC5593426.xml
new file mode 100644
index 0000000..f30cccb
--- /dev/null
+++ b/tests/fixtures/jats/PMC5593426.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="utf-8"?>
+<article><front><article-meta><article-id pub-id-type="pmcid">PMC5593426</article-id><article-id pub-id-type="pmcid-ver">PMC5593426.1</article-id><article-id pub-id-type="pmcaid">5593426</article-id><article-id pub-id-type="pmcaiid">5593426</article-id><article-id pub-id-type="manuscript-id">NIHMS871459</article-id><article-id pub-id-type="pmid">28530713</article-id><article-id pub-id-type="doi">10.1038/ni.3753</article-id><article-id pub-id-type="manuscript-id-alternative">NIHMS871459</article-id><article-id pub-id-type="manuscript-id-alternative">NIHPA871459</article-id><title-group><article-title>BACH2 immunodeficiency illustrates an association between super-enhancers and haploinsufficiency</article-title></title-group><permissions><license><license-p>Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:
+<uri xlink:href="http://www.nature.com/authors/editorial_policies/license.html#terms" xmlns:xlink="http://www.w3.org/1999/xlink">http://www.nature.com/authors/editorial_policies/license.html#terms</uri></license-p></license></permissions></article-meta></front><floats-group><table-wrap id="T1" orientation="portrait" position="float"><label>Table 1</label><caption><p>Summary clinical characteristics of patients with missense mutations in BACH2.</p></caption><table frame="below" rules="groups"><thead><tr><th align="left" colspan="1" rowspan="1" valign="top"/><th align="left" colspan="3" rowspan="1" valign="bottom">
+<hr/></th></tr><tr><th align="left" colspan="1" rowspan="1" valign="top"/><th align="center" colspan="3" rowspan="1" valign="top">Patients</th></tr><tr><th align="left" colspan="4" rowspan="1" valign="bottom">
+<hr/></th></tr><tr><th align="left" colspan="1" rowspan="1" valign="top">Demographic and clinical characteristics</th><th align="left" colspan="1" rowspan="1" valign="top">A.II.1</th><th align="left" colspan="1" rowspan="1" valign="top">B.II.1</th><th align="left" colspan="1" rowspan="1" valign="top">B.III.2</th></tr></thead><tbody><tr><td align="left" colspan="1" rowspan="1" valign="top">Age, Sex</td><td align="left" colspan="1" rowspan="1" valign="top">19, F</td><td align="left" colspan="1" rowspan="1" valign="top">63, M</td><td align="left" colspan="1" rowspan="1" valign="top">40,F</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">Lymphadenopathy</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">Splenomegaly</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">No</td><td align="left" colspan="1" rowspan="1" valign="top">No</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">Intestinal manifestations</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> Chronic diarrhea</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> IBD</td><td align="left" colspan="1" rowspan="1" valign="top">Colitis</td><td align="left" colspan="1" rowspan="1" valign="top">Not biopsied</td><td align="left" colspan="1" rowspan="1" valign="top">UC aged 10; Crohn’s aged 32</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">Pulmonary manifestations</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> Recurrent sino-pulmonary infections</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> Radiographic changes on chest CT</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Not imaged</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">Immunoglobulins<xref ref-type="table-fn" rid="TFN2">†</xref></td><td align="left" colspan="1" rowspan="1" valign="top"/><td align="left" colspan="1" rowspan="1" valign="top"/><td align="left" colspan="1" rowspan="1" valign="top"/></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> IgM</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">High</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> IgG</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">High<xref ref-type="table-fn" rid="TFN3">*</xref></td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> IgA</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> IgE</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Low</td><td align="left" colspan="1" rowspan="1" valign="top">Normal</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top"> On IvIg treatment</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">Yes</td><td align="left" colspan="1" rowspan="1" valign="top">No</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">EBV antibodies</td><td align="left" colspan="1" rowspan="1" valign="top">N/A (DNA negative)</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">High</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">RhF</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">dsDNA antibodies</td><td align="left" colspan="1" rowspan="1" valign="top">Negative</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">ANCA</td><td align="left" colspan="1" rowspan="1" valign="top">Positive (pANCA)<xref ref-type="table-fn" rid="TFN4">‡</xref></td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td></tr><tr><td align="left" colspan="1" rowspan="1" valign="top">ANA</td><td align="left" colspan="1" rowspan="1" valign="top">Negative</td><td align="left" colspan="1" rowspan="1" valign="top">N/A</td><td align="left" colspan="1" rowspan="1" valign="top">Negative</td></tr></tbody></table><table-wrap-foot><fn id="TFN1"><p>IvIg, intravenous immunoglobulin; EBV, Epstein-Barr virus; RhF, rheumatoid factor, dsDNA, double-stranded DNA; ANCA, anti-neutrophil cytoplasmic antibody; p-ANCA, perinuclear ANCA; ANA, antinuclear antibody; UC, ulcerative colitis; N/A not assessed.</p></fn><fn id="TFN2"><label>†</label><p>Absolute values given in <xref ref-type="supplementary-material" rid="SD6">Supplementary Table 1</xref>;</p></fn><fn id="TFN3"><label>*</label><p>progressive decline in IgG;</p></fn><fn id="TFN4"><label>‡</label><p>positive by immunofluorescence but negative for myeloperoxidase and proteinase III antibodies by ELISA.</p></fn></table-wrap-foot></table-wrap></floats-group></article>
diff --git a/tests/fixtures/jats/README.md b/tests/fixtures/jats/README.md
new file mode 100644
index 0000000..e4354f8
--- /dev/null
+++ b/tests/fixtures/jats/README.md
@@ -0,0 +1,21 @@
+# JATS regression fixture
+
+`PMC5593426.xml` retains Table 1, article identifiers/title and the original
+permissions from the Europe PMC response for PMID:28530713 / PMC5593426,
+downloaded 2026-09-15 from:
+https://www.ebi.ac.uk/europepmc/webservices/rest/PMC5593426/fullTextXML
+
+Full downloaded response SHA-256:
+`f9512138d416f28467b81373fd1157766c868ca90bbf6129933ea3b968912ae7`
+
+The article is *BACH2 immunodeficiency illustrates an association between
+super-enhancers and haploinsufficiency*, DOI:10.1038/ni.3753.
+Table 1 contains the immunoglobulin findings reported in issue #68. Its source
+`table-wrap` (T1), including caption, rows and notes, is preserved inside a
+minimal article with the original `floats-group` placement. BeautifulSoup's XML
+serializer normalized markup; table text and attributes were not edited.
+Article prose, other figures, references and supplementary material are omitted.
+
+The original permissions remain in the excerpt. Only the relevant table and
+provenance metadata are retained for regression testing; the complete manuscript
+is not included and the excerpt is not relicensed.
diff --git a/tests/test_jats_tables.py b/tests/test_jats_tables.py
new file mode 100644
index 0000000..d2c6a9a
--- /dev/null
+++ b/tests/test_jats_tables.py
@@ -0,0 +1,344 @@
+"""JATS table extraction and targeted cache migration regressions for #68."""
+
+from pathlib import Path
+
+import pytest
+
+from linkml_reference_validator.etl.extract.xml import XMLExtractor
+from linkml_reference_validator.etl.reference_fetcher import ReferenceFetcher
+from linkml_reference_validator.models import (
+    FullTextLocation,
+    ReferenceContent,
+    ReferenceValidationConfig,
+)
+from linkml_reference_validator.validation.supporting_text_validator import (
+    SupportingTextValidator,
+)
+
+FIXTURE = Path(__file__).parent / "fixtures/jats/PMC5593426.xml"
+
+
+def test_real_clinical_rows():
+    """The reported table-only findings are directly quotable from the real paper."""
+    text = XMLExtractor().extract(FIXTURE.read_bytes())
+    assert text is not None
+    assert (
+        "## Table 1 Summary clinical characteristics of patients with missense mutations in BACH2."
+        in text
+    )
+    assert "IvIg, intravenous immunoglobulin" in text
+    for row in [
+        "On IvIg treatment | Yes | Yes | No",
+        "IgM | Low | Low | High",
+        "IgG | Low | Low | High*",
+    ]:
+        assert f"| {row} |" in text
+        ref = ReferenceContent(reference_id="PMID:28530713", content=text)
+        assert (
+            SupportingTextValidator(ReferenceValidationConfig())
+            .find_text_in_reference(row, ref)
+            .found
+        )
+
+
+@pytest.mark.parametrize("placement", ["body", "floats-group"])
+def test_structural_tables(placement):
+    """Wrappers, blocks and inline tags retain boundaries without duplicate captions."""
+    xml = f"""<article><abstract><p>Abstract stays separate.</p></abstract><{placement}>
+    <table-wrap><label>Table 2</label><caption><p>Clinical <italic>features</italic>.</p></caption>
+    <alternatives><table><tbody><tr><th>Patient</th><th>A</th><th>B</th></tr>
+    <tr><td><p>CD<sup>4</sup><sup>+</sup> cells</p><p>Ig<italic>G</italic></p></td>
+    <td>Yes<break/>again</td><td>A | B</td></tr></tbody></table></alternatives>
+    </table-wrap></{placement}></article>"""
+    text = XMLExtractor().extract(xml)
+    assert (
+        text
+        == "## Table 2 Clinical features.\n\n| Patient | A | B |\n| CD4+ cells IgG | Yes again | A \\| B |"
+    )
+
+
+def test_nested_tables_and_wraps_once():
+    """Each actual table owns its rows; descendants never leak into ancestor cells."""
+    xml = """<article><body><p>Body.</p><table-wrap><label>Outer</label><table>
+    <tr><td>Outer cell<table-wrap><label>Inner</label><table><tr><td>Inner cell</td></tr></table>
+    </table-wrap></td></tr></table></table-wrap></body></article>"""
+    text = XMLExtractor().extract(xml)
+    assert text == "Body.\n\n## Outer\n\n| Outer cell |\n\n## Inner\n\n| Inner cell |"
+
+
+def test_spans_are_explicit_source_cells():
+    """Spanned cells are annotated, never propagated into invented patient values."""
+    xml = """<article><table-wrap><table><tr><td rowspan="2">Group</td><td colspan="2">Shared</td></tr>
+    <tr><td>A</td><td>B</td></tr></table></table-wrap></article>"""
+    assert (
+        XMLExtractor().extract(xml)
+        == "## Table\n\n| Group [rowspan=2] | Shared [colspan=2] |\n| A | B |"
+    )
+
+
+@pytest.mark.parametrize("count", [200, 201])
+def test_row_cap(count):
+    """Only the first 200 source rows survive, with an explicit truncation notice."""
+    rows = "".join(f"<tr><td><p>Row {i}</p></td></tr>" for i in range(count))
+    text = XMLExtractor().extract(
+        f"<article><body><table-wrap><table>{rows}</table></table-wrap></body></article>"
+    )
+    assert text.count("\n| Row ") == 200
+    assert "| Row 199 |" in text
+    assert "Row 200" not in text
+    assert ("[Table truncated after 200 rows.]" in text) == (count > 200)
+
+
+def test_stub_is_checked_before_tables():
+    """Table size cannot disguise a restricted body notice."""
+    xml = "<article><body><p>Text cannot be obtained from PMC.</p></body><table-wrap><table>"
+    xml += "<tr><td>Data</td></tr>" * 200 + "</table></table-wrap></article>"
+    assert XMLExtractor().extract(xml) is None
+
+
+def make_fetcher(tmp_path):
+    """Use a fresh in-memory cache on each call."""
+    return ReferenceFetcher(
+        ReferenceValidationConfig(cache_dir=tmp_path, rate_limit_delay=0)
+    )
+
+
+@pytest.mark.parametrize("version", [None, 0, 1, 99])
+def test_xml_version_roundtrip(tmp_path, version):
+    """Metadata-only rewrites neither certify old XML nor downgrade future stamps."""
+    fetcher = make_fetcher(tmp_path)
+    path = fetcher.get_cache_path("unknown:xml")
+    stamp = "" if version is None else f"xml_extraction_version: {version}\n"
+    path.write_text(
+        "---\nreference_id: unknown:xml\nextractor_version: 1\ncontent_type: full_text_xml\n"
+        + stamp
+        + "---\nOld body"
+    )
+    ref = fetcher._load_from_disk("unknown:xml", allow_stale=True)
+    fetcher._save_to_disk(ref)
+    assert ReferenceFetcher._is_stale_cache_entry(path.read_text()) == (
+        version in (None, 0)
+    )
+    assert ref.metadata.get("xml_extraction_version") == version
+    if version is None:
+        assert "xml_extraction_version" not in path.read_text()
+
+
+def test_xml_offline_stays_stale(tmp_path, caplog):
+    """Useful old XML remains available offline without falsely certifying its text."""
+    fetcher = make_fetcher(tmp_path)
+    path = fetcher.get_cache_path("unknown:xml")
+    old = "---\nreference_id: unknown:xml\nextractor_version: 1\ncontent_type: full_text_xml\n---\nOld body"
+    path.write_text(old)
+    assert fetcher.fetch("unknown:xml").content == "Old body"
+    assert path.read_text() == old
+    assert "older extractor" in caplog.text
+    assert fetcher._load_from_disk("unknown:xml") is None
+
+
+def test_provider_xml_stamp_and_abstract(tmp_path):
+    """Fresh extracted provider XML certifies its version and keeps the abstract."""
+    fetcher = make_fetcher(tmp_path)
+    ref = ReferenceContent(
+        reference_id="unknown:xml",
+        content="Original abstract",
+        content_type="abstract_only",
+    )
+    text = XMLExtractor().extract(FIXTURE.read_bytes())
+    assert fetcher.apply_full_text_location(
+        ref, FullTextLocation(text=text, format_hint="xml"), "pmc"
+    )
+    assert ref.content.startswith("Original abstract\n\n")
+    assert ref.metadata["xml_extraction_version"] == 1
+    assert make_fetcher(tmp_path)._load_from_disk(ref.reference_id) is not None
+
+
+def test_warm_legacy_xml_refreshes_from_real_source(tmp_path, monkeypatch):
+    """A registered fixture-backed source replaces legacy text once, then stays warm."""
+    from linkml_reference_validator.etl.sources.base import (
+        ReferenceSource,
+        ReferenceSourceRegistry,
+    )
+
+    reads = []
+
+    class FixtureXMLSource(ReferenceSource):
+        """Read and extract the actual PMC response using the source contract."""
+
+        @classmethod
+        def prefix(cls):
+            """Use an isolated reference namespace."""
+            return "JATSFIXTURE"
+
+        def fetch(self, identifier, config):
+            """Perform real extraction, tracking disk acquisitions."""
+            reads.append(identifier)
+            return ReferenceContent(
+                reference_id=f"JATSFIXTURE:{identifier}",
+                content=XMLExtractor().extract(FIXTURE.read_bytes()),
+                content_type="full_text_xml",
+            )
+
+    monkeypatch.setattr(ReferenceSourceRegistry, "_sources", [FixtureXMLSource])
+    fetcher = make_fetcher(tmp_path)
+    path = fetcher.get_cache_path("JATSFIXTURE:28530713")
+    path.write_text(
+        "---\nreference_id: JATSFIXTURE:28530713\nextractor_version: 1\ncontent_type: full_text_xml\n---\nLegacy prose only"
+    )
+    fresh = fetcher.fetch("JATSFIXTURE:28530713")
+    assert "| On IvIg treatment | Yes | Yes | No |" in fresh.content
+    assert fresh.metadata["xml_extraction_version"] == 1
+    assert "xml_extraction_version: 1" in path.read_text()
+    assert make_fetcher(tmp_path).fetch("JATSFIXTURE:28530713").content == fresh.content
+    assert reads == ["28530713"]
+
+
+@pytest.mark.parametrize(
+    "kind,stamp",
+    [("full_text_pdf", ""), ("full_text_html", "html_full_text_version: 1\n")],
+)
+def test_xml_migration_does_not_refresh_other_formats(tmp_path, kind, stamp):
+    """Current HTML and PDF caches remain usable without an XML version."""
+    fetcher = make_fetcher(tmp_path)
+    path = fetcher.get_cache_path("unknown:other")
+    path.write_text(
+        f"---\nreference_id: unknown:other\nextractor_version: 1\ncontent_type: {kind}\n{stamp}---\nCurrent body"
+    )
+    assert fetcher._load_from_disk("unknown:other").content == "Current body"
+
+
+def test_downloaded_xml_provider_uses_tables(tmp_path):
+    """Actual HTTP acquisition extracts the PMC fixture and stamps its cache."""
+    from functools import partial
+    from http.server import SimpleHTTPRequestHandler, ThreadingHTTPServer
+    from threading import Thread
+
+    server = ThreadingHTTPServer(
+        ("127.0.0.1", 0),
+        partial(SimpleHTTPRequestHandler, directory=str(FIXTURE.parent)),
+    )
+    thread = Thread(target=server.serve_forever, daemon=True)
+    thread.start()
+    try:
+        ref = ReferenceContent(
+            reference_id="unknown:download",
+            content_type="abstract_only",
+            content="Abstract",
+        )
+        fetcher = make_fetcher(tmp_path)
+        assert fetcher.apply_full_text_location(
+            ref,
+            FullTextLocation(
+                url=f"http://127.0.0.1:{server.server_port}/{FIXTURE.name}",
+                format_hint="xml",
+            ),
+            "local-test",
+        )
+        assert ref.content.startswith("Abstract\n\n")
+        assert "| On IvIg treatment | Yes | Yes | No |" in ref.content
+        assert ref.metadata["xml_extraction_version"] == 1
+        assert not fetcher._is_stale_cache_entry(
+            fetcher.get_cache_path(ref.reference_id).read_text()
+        )
+    finally:
+        server.shutdown()
+        server.server_close()
+        thread.join()
+
+
+def test_hidden_xml_nodes_are_not_quotable():
+    """Comments and processing instructions are metadata, while CDATA is content."""
+    xml = """<article><table-wrap><caption><p>Clinical<!-- hidden caption --></p></caption>
+    <table><tr><td>Yes<!-- secret --><?review hidden?> again</td>
+    <td><![CDATA[Useful text]]></td><td/></tr></table></table-wrap></article>"""
+    assert (
+        XMLExtractor().extract(xml) == "## Clinical\n\n| Yes again | Useful text |  |"
+    )
+
+
+@pytest.mark.parametrize("placement", ["body", "floats-group"])
+def test_table_footnotes_preserved_once(placement):
+    """Footnotes defining table markers remain quotable, including floats-group notes."""
+    xml = f"""<article><{placement}><table-wrap><label>Table 1</label>
+    <table><tr><td>IgG</td><td>High<sup>*</sup></td></tr></table>
+    <table-wrap-foot><fn><p>* Measured before <italic>treatment</italic>.</p></fn>
+    <fn><p>IvIg, intravenous immunoglobulin.</p></fn></table-wrap-foot>
+    </table-wrap></{placement}></article>"""
+    assert XMLExtractor().extract(xml) == (
+        "## Table 1\n\n| IgG | High* |\n\n"
+        "* Measured before treatment. IvIg, intravenous immunoglobulin."
+    )
+
+
+def test_nested_wrapper_footnotes_are_not_duplicated():
+    """Inner and outer notes are rendered once, under their own wrappers."""
+    xml = """<article><body><table-wrap><table><tr><td>Outer</td></tr></table>
+    <table-wrap><table><tr><td>Inner</td></tr></table><table-wrap-foot><p>Inner note.</p></table-wrap-foot></table-wrap>
+    <table-wrap-foot><p>Outer note.</p></table-wrap-foot></table-wrap></body></article>"""
+    text = XMLExtractor().extract(xml)
+    assert text.count("Inner note.") == 1
+    assert text.count("Outer note.") == 1
+
+
+@pytest.mark.parametrize("tag", ["sub-article", "response"])
+def test_other_article_tables_are_not_attributed_to_main_paper(tag):
+    """Review/reply tables cannot become evidence attributed to the main article."""
+    xml = f"""<article><body><p>Main prose.</p></body>
+    <floats-group><table-wrap><table><tr><td>Main finding</td></tr></table></table-wrap></floats-group>
+    <{tag}><body><p>Reviewer prose.</p></body><table-wrap><table><tr><td>Reviewer finding</td></tr></table>
+    <table-wrap-foot><p>Reviewer note.</p></table-wrap-foot></table-wrap></{tag}></article>"""
+    text = XMLExtractor().extract(xml)
+    assert text == "Main prose.\n\n## Table\n\n| Main finding |"
+
+
+def test_nested_table_without_own_wrapper_has_own_heading():
+    """A nested physical table must not repeat the outer table's label/caption."""
+    xml = """<article><table-wrap><label>Table 1</label><caption><p>Main caption</p></caption>
+    <table><tr><td>Outer<table><tr><td>Nested</td></tr></table></td></tr></table></table-wrap></article>"""
+    assert (
+        XMLExtractor().extract(xml)
+        == "## Table 1 Main caption\n\n| Outer |\n\n## Nested table\n\n| Nested |"
+    )
+
+
+@pytest.mark.parametrize(
+    "table", ['<graphic href="T1.jpg"/>', "<table/>", "<table><tr/></table>"]
+)
+def test_unrenderable_table_keeps_caption(table):
+    """Existing caption evidence survives even when no table cells can be extracted."""
+    xml = f"<article><body><table-wrap><label>Table 1</label><caption><p>Baseline characteristics.</p></caption>{table}</table-wrap></body></article>"
+    assert XMLExtractor().extract(xml) == "## Table 1 Baseline characteristics."
+
+
+@pytest.mark.parametrize("tag", ["sub-article", "response"])
+def test_floats_only_article_does_not_take_reviewer_body(tag):
+    """A missing main body must not select a reviewer body as fallback prose."""
+    xml = f"<article><floats-group><table-wrap><table><tr><td>Main finding</td></tr></table></table-wrap></floats-group><{tag}><body><p>Reviewer prose.</p></body></{tag}></article>"
+    assert XMLExtractor().extract(xml) == "## Table\n\n| Main finding |"
+
+
+def test_cell_boundary_contracts():
+    """Unit spans are implicit, backslashes escaped, and sup/sub text stays flattened."""
+    xml = r'<article><table-wrap><table><tr><td rowspan="1" colspan="1">A\B</td><td>10<sup>9</sup></td><td>H<sub>2</sub>O</td></tr></table></table-wrap></article>'
+    assert XMLExtractor().extract(xml) == "## Table\n\n| A\\\\B | 109 | H2O |"
+
+
+def test_bare_table_is_outside_jats_wrapper_contract():
+    """Non-JATS layout tables are not interpreted as article evidence."""
+    assert (
+        XMLExtractor().extract(
+            "<article><table><tr><td>Cell</td></tr></table></article>"
+        )
+        is None
+    )
+
+
+def test_unrendered_wrapper_paragraphs_remain_body_prose():
+    """Existing alternative/attribution paragraphs survive unless rendered elsewhere."""
+    xml = """<article><body><p>Body.</p><table-wrap><label>Table 1</label>
+    <caption><p>Caption.</p></caption><attrib><p>Source attribution.</p></attrib>
+    <table><tr><td><p>Cell</p></td></tr></table></table-wrap></body></article>"""
+    assert (
+        XMLExtractor().extract(xml)
+        == "Body.\n\nSource attribution.\n\n## Table 1 Caption.\n\n| Cell |"
+    )