biosemantics / etc-site-archived-do-not-use

Source code for the ETC Toolkit web application
http://etc.cs.umb.edu/etcsite/
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Content between "&lt" and "gt" doesn't appear in the Context #630

Open CathyYujie opened 7 years ago

CathyYujie commented 7 years ago

xml file: image

in the Text Capture:(show information of based) Problem: the content between "&lt" and "&gt" and around is gone in the context however, these contents are stored in the system dataset and are analyzed to be characters image

The problem in the Matrix generation has been solved: https://github.com/biosemantics/etc-site/issues/611

CathyYujie commented 7 years ago

<?xml version="1.0" encoding="UTF-8"?>

Lawrence A. Alice,Douglas H. Goldman,James A. Macklin,Gerry Moore unknown rosaceae rosoideae rubeae rubus Sp. Pl. 1: 492. 1753 * Bramble Gen. Pl. ed. 5, 218. 1754 family rosaceae;subfamily rosoideae;tribe rubeae;genus rubus [Ancient Latin name for bramble, from ruber , red] Dalibarda 2. Shrubs, subshrubs, or herbs, perennial, 0.5-30(-50) dm; fibrous, more or less woody in species with larger plants. Stems 1-several, <biennial or perennial, rarely annual (R. illecebrosus)>, erect, arching, mounding, or creeping, rarely decumbent, ascending, or scrambling, <rooting or not at nodes or tips, terete or angled>; <prickles absent or sparse to dense, erect to retrorse, weak to stout, broad based or not; bristles absent or sparse to dense, erect to slightly retrorse, weak to stiff>; glabrous or hairy, eglandular or stipitate-glandular, sometimes sessile-glandular, <pruinose or not>. Leaves winter-persistent to deciduous, cauline; stipules filiform or elliptic to ovate, margins entire; petiole present; blade reniform to orbiculate, 2–30 cm, herbaceous to more or less coriaceous, leaflets 0 or 3, 5, 7, or 9, terminal ovate to elliptic to obovate, <1.7-15 cm, base cuneate to rounded or cordate, sometimes truncate, rarely tapered or obtuse, unlobed or lobed>, margins flat or revolute, finely to coarsely crenate, dentate to doubly dentate, or serrate to doubly serrate, abaxial surface <unarmed or with prickles on midvein consistent with those on stems>, glabrous or more or less densely hairy, eglandular or more or less densely stipitate-glandular, sometimes sessile-glandular, along veins. Inflorescences axillary or terminal, 1-35(-100)-flowered, cymiform, racemiform, umbelliform, thyrsiform, or paniculiform, glabrous or sparsely to densely pubescent, <eglandular or sparsely to densely glandular, armed or unarmed>; bracts usually present; bracteoles absent. Pedicels present, <unarmed or sparsely armed with prickles similar to those of stems, glabrous or sparsely to densely hairy, eglandular or sparsely to densely stipitate-glandular, sometimes sessile-glandular>. Flowers bisexual (unisexual in R. chamaemorus, R. ursinus, and subg. Micranthobatus [in the sense of Kalkman]), 5-80 mm diam.; hypanthium 3-10 mm diam., glabrous or sparsely to densely pubescent, <eglandular or sparsely to densely glandular>; sepals 5, erect or spreading to reflexed, lanceolate to long-caudate, <unarmed or armed, glabrous or hairy, eglandular or sparsely to densely stipitate-glandular, sometimes sessile-glandular>; petals (0-)5(or 6), white to pink or magenta, suborbiculate to elliptic, obovate, or spatulate; stamens 20-100 more, shorter to longer than petals, <filaments filiform or laminar>; carpels glabrous or hairy, <styles slender or clavate>. Fruits aggregated drupelets, (1-)5-100[-150], <not or weakly to strongly coherent>, separating with or without torus attached, golden yellow to red or black, globose to hemispheric or cylindric, 5-20 mm, <fleshy or dryish>, glabrous or finely hairy, <sometimes pruinose>; hypanthium usually persistent; sepals usually persistent, usually reflexed. Seeds 1 per drupelet. x = 7. North America, Mexico, West Indies, Central America, South America, Eurasia, Africa, Pacific Islands (Hawaii, New Zealand), Australia; introduced widely. Species 250–700 (37 in the flora): Molecular data (L. A. Alice and C. S. Campbell 1999) have shown Rubus to be monophyletic when including Dalibarda (R. repens). These data also show that long-recognized infrageneric taxa, such as the raspberries (subg. Idaeobatus Focke) and dwarf raspberries [subg. Cylactis (Rafinesque) Focke], may not be monophyletic. Although species are not organized here according to subgenera, they would belong to L. H. Bailey’s (1941–1945) subgeneric treatment as follows: flowering raspberries or thimbleberries [subg. Anoplobatus (Focke) Focke, species 3, 9, 18, 22, 23], snow raspberries [subg. Chamaebatus (Focke) Focke, species 19], cloudberries or baked-apple berries [subg. Chamaemorus (Hill) Focke, species 7], dwarf raspberries or plumboys (subg. Cylactis, species 2, 16, 26, 29, 31), raspberries (subg. Idaeobatus, species 11, 13, 14, 17, 20, 21, 24, 28, 33), and blackberries (subg. Rubus, species 1, 4–6, 8, 10, 12, 15, 25, 27, 32, 34, 35, 36, 37). Bailey did not include Dalibarda repens (30. R. repens) in Rubus, but W. O. Focke (1910) included it in subg. Dalibarda (under the illegitimate name R. dalibarda Linnaeus). Rubus, especially the blackberries, presents some of the most difficult species-level problems, because of polyploidy, apomixis, and hybridization. As a result, differences of opinion on the number of species to be recognized from a given region can vary tremendously (for example, treatments in M. L. Fernald 1950 and H. A. Gleason and A. Cronquist 1991 for the northern half of the eastern United States plus parts of southeastern Canada, the former recognizing 205 species, the latter 25). A relatively conservative approach is taken here, one with much precedent (for example, A. E. Radford et al. 1968; R. G. Brown and M. L. Brown 1972; R. K. Godfrey and J. W. Wooten 1981; E. G. Voss 1972–1996, vol. 2; Great Plains Flora Association 1986; Godfrey 1988; Gleason and Cronquist; A. F. Rhoads and W. M. Klein 1993; E. B. Smith 1994; R. S. Mitchell and G. C. Tucker 1997; R. P. Wunderlin 1998; D. W. Magee and H. E. Ahles 1999; T. S. Cooperrider et al. 2001; R. L. Jones 2005; A. S. Weakley 2012; Weakley et al. 2012). The decision to treat Rubus conservatively herein is due in part to the broad geographic distribution of many species in which quantitative characters are highly variable and the general absence of empirical data demonstrating that minor morphological variants are genetically based and not environmentally plastic. There is an overall lack of comprehensive herbarium specimens (for example, primocane, floricane with flowers and/or fruits, and habit data) making study difficult. Regarding Rubus, R. K. Godfrey (1988) wrote, "oversimplification appears to be the only way to achieve a practicable solution to the dilemma." Other genera present a similar predicament by containing a large number of microspecies, such as Alchemilla, Crepis, Hieracium, Oenothera, and Taraxacum. W. Dietrich et al. (1997) stated for Oenothera taxonomy, and equally applicable to Rubus, that "immense splitting would result in a taxonomic system where even the specialist would lose the overview." See P. A. Rydberg (1913c), L. H. Bailey (1941–1945), P. D. Strausbaugh and E. L. Core (1978), H. A. Davis (1990), and M. P. Widrlechner (1998) for Rubus treatments that recognize many species. Definitions for two morphologic terms primarily associated with Rubus are: primocane, a biennial or perennial stem prior to being developed enough for flowering, with flowering not occurring until at least its second season of growth, and floricane, a biennial or perennial stem after it has begun flowering, which does not occur until at least its second season of growth (R. W. Kiger and D. M. Porter 2001). Parcifrond is an elongate, sparsely leafy, sterile branch arising from a floricane proximal to its flowering branches. Novirame is a fertile (flowering, fruiting) branch on a primocane. Descriptions in this treatment are based on primocanes and floricanes, and exclude parcifronds and novirames. In key leads and descriptions in this treatment, references to leaves are for those on primocanes, unless otherwise indicated. Also, for stems unsupported by other vegetation, measurements of vertical distances above the ground are given, not stem lengths. For example, stems of Rubus flagellaris may be as much as 3 dm above the ground even though the stems may be several meters long. Rubus inflorescences have been described as cymose or racemose. The inflorescences are determinate (thus cymose), with the terminal flower opening first. Flowering then proceeds acropetally (J. C. Guillard 1857; H. W. Rickett 1944), a pattern that is more typical of racemes. In the treatment here, inflorescences are described as cymiform, umbelliform, paniculiform, racemiform, or thyrsiform, these characterizations based on what the inflorescence most closely resembles. Also, inflorescence descriptions here refer to the flowering structures that generally terminate a branch distal to the leaves on that branch, including undivided, smaller, bractlike leaves. In plants with racemiform, paniculiform, or thyrsiform inflorescences, smaller axillary inflorescences containing one to few flowers are common and typically occur just proximal to the main inflorescences. Although most Rubus species in the flora area bear inflorescences that terminate a branch, such inflorescences often can appear to be axillary if terminating very short, leafy, axillary branches. Especially in subg. Rubus, terminal inflorescences almost always form on lateral branches, but occasionally form on a distal extension of the primocane of the previous year. In the flora area, native species in subg. Rubus have shorter floricanes, generally less than 30 cm; most non-native members in the flora area can have floricane branches exceeding 1 m. Rubus shows diversity in armature and glands. Prickles, which protect the plant and aid some species in climbing, range from stout and broad-based to weak and narrow-based. Bristles may be stiff or weak. Prickles and bristles range from erect to retrorse. Generally, plants with sparse armature have spaces between the prickle bases or bristles that are more than 2–3 times the length of the prickles or bristles; plants with dense armature have spaces that are equal to or less than lengths. Glands vary significantly in size and shape and can be stalked or sessile. Glandularity is not always obvious; glands are sometimes hidden by other hairs or can be very small. Sessile glands can be less than 0.2 mm long or wide, requiring a good lens to be viewed; they are spheric to obovoid, whereas stipitate glands can be spheric to obovoid or discoid to cupulate. Cultivars of blackberries and raspberries are grown for their edible fruit, and other Rubus taxa are grown for their ornamental value. Cultivars of blackberries have parentages or origins that include species native to North America and Europe, as well as red raspberry (for example, R. idaeus subsp. idaeus and subsp. strigosus) (J. R. Clark et al. 2007). Cultivars of red and black raspberries are primarily derived from R. idaeus and R. occidentalis, respectively. Purple raspberry cultivars are derived from the crossing of red and black raspberries. In both black and red raspberries, a lack of anthocyanin pigments can lead to the production of yellowish fruit. Cultivars of R. idaeus with yellowish fruit are sold as golden or amber raspberries. The Logan and Boysen cultivars are widely grown for their excellent fruits. Both cultivars are polyploid (6x and 8x respectively) involving R. ursinus as the maternal parent. In Loganberry, the paternal parent is R. idaeus subsp. idaeus, while Boysenberry has a more complicated ancestry. Due to horticultural or agricultural interest, it can be expected that more Rubus species will be introduced into the flora, with some naturalizing. Rubus tomentosus Borkhausen var. canescens (de Candolle) Wirtgen, a European species similar to R. bifrons and R. vestitus but much more pubescent than either, was reported growing wild in a small area in Randolph County, West Virginia (E. E. Hutton and R. B. Clarkson 1961), although more recently it has not been confirmed as naturalized there (P. J. Harmon et al. 2006). Rubus hirsutus Thunberg, native of China, Japan, and the Korean peninsula (L. Lingdi and D. E. Boufford 2003), was found naturalized in a woodland in Chapel Hill, North Carolina (D. H. Goldman, pers. obs.). Alice, L. A. and C. S. Campbell. 1999. Phylogeny of Rubus (Rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Amer. J. Bot. 86: 81–97. Bailey, L. H. 1941–1945. Species batorum. The genus Rubus in North America (north of Mexico) I–X. Gentes Herb. 5: 1–918. Davis, H. A. 1990. Studies in Rubus. Castanea 55: 22–30. Davis, H. A., A. M. Fuller, and T. Davis. 1967–1970. Contributions towards the revision of eubati of eastern North America. Castanea 32: 20–37; 33: 50–76, 206–241; 34: 157–179, 235–266; 35: 176–194. Widrlechner, M. P. 1998. The genus Rubus L. in Iowa. Castanea 63: 415–465.