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There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with biomedical data. When metadata are not well-structured or precise, the associated data are harder to find and are often burdensome to reuse, analyze or integrate with other datasets due to the upfront curation effort required to make the data usable -- typically through retrospective standardization and cleaning of the (meta)data. With the goal of facilitating the task of standardizing metadata -- either in bulk or in a one-by-one fashion; for example, to support auto-completion of biomedical entities in forms -- we have developed an open-source tool called text2term that maps free-text descriptions of biomedical entities to controlled terms in ontologies. The tool is highly configurable and can be used in multiple ways that cater to different users and expertise levels -- it is available on PyPI and can be used programmatically as any Python package; it can also be used via a command-line interface; or via our hosted, graphical user interface-based Web application (https://text2term.hms.harvard.edu); or by deploying a local instance of our interactive application using Docker.

Soft hairs are an intrinsic infrared feature of a black hole, which may also affect near-horizon physics. In this work, we study some of the subtleties surrounding one of the primary observables with which we can study their effects in the context of Einstein's gravity: the black hole shadow. First, we clarify the singular pathology associated with black holes with soft hairs and demonstrate that the metrics of linearly superrotated black holes are free of near-zone pathologies due to appropriate asymptotic falloff conditions being imposed on the event horizon. We then analytically construct the photon orbits around such black holes, derive the shadow equation for near-zone observers, and find that the linear superrotation hairs deform the circular shadow of a bald Schwarzchild black hole into an ellipse. This is in sharp contrast to their supertranslated counterparts, which only shift the position of the center of the circular shadow but do not change its shape. Our results suggest a richness to the observable effects due to the infrared structures of Einstein's gravity., Comment: 10 pages, 3 figures, v3. Provided a brief review of the methodology used for the shadow construction. Clarify the limitations on the type of observer relevant to our results. Updated and added figures to provide a broader view of the valient features of the FPOs and shadows. The main result of the shadow deformation does not change

In this pedagogical article, we explore a powerful language for describing the notion of spacetime and particle dynamics intrinsic to a given fundamental physical theory, focusing on special relativity and its Newtonian limit. The starting point of the formulation is the representations of the relativity symmetries. Moreover, that seriously furnishes -- via the notion of symmetry contractions -- a natural way in which one can understand how the Newtonian theory arises as an approximation to Einstein's theory. We begin with the Poincar\'{e} symmetry underlying special relativity and the nature of Minkowski spacetime as a coset representation space of the algebra and the group. Then, we proceed to the parallel for the phase space of a spin zero particle, in relation to which we present the full scheme for its dynamics under the Hamiltonian formulation, illustrating that as essentially the symmetry feature of the phase space geometry. Lastly, the reduction of all that to the Newtonian theory as an approximation with its space-time, phase space, and dynamics under the appropriate relativity symmetry contraction is presented. While all notions involved are well established, the systematic presentation of that story as one coherent picture fills a gap in the literature on the subject matter., Comment: proof-corrected final version: 31 latex pages, no figure

In this article, we utilize the insights gleaned from our recent formulation of space(-time), as well as dynamical picture of quantum mechanics and its classical approximation, from the relativity symmetry perspective in order to push further into the realm of the proposed fundamental relativity symmetry $SO(2,4)$ of our quantum relativity project. We explicitly trace how the diverse actors in this story change through various contraction limits, paying careful attention to the relevant physical units, in order to place all known relativity theories -- quantum and classical -- within a single framework. More specifically, we explore both of the possible contractions of $SO(2,4)$ and its coset spaces in order to determine how best to recover the lower-level theories. These include both new models and all familiar theories, as well as quantum and classical dynamics with and without Einsteinian special relativity. Along the way, we also find connections with covariant quantum mechanics. The emphasis of this article rests on the ability of this language to not only encompass all known physical theories, but to also provide a path for extensions. It will serve as the basic background for more detailed formulations of the dynamical theories at each level, as well as the exact connections amongst them., Comment: 38 pages, 2 tables, published version

With approaching quantum/noncommutative models for the deep microscopic spacetime in mind, and inspired by our recent picture of the (projective) Hilbert space as the model of physical space behind basic quantum mechanics, we reformulate here the WWGM formalism starting from the canonical coherent states and taking wavefunctions as expansion coefficients in terms of this basis. This provides us with a transparent and coherent story of simple quantum dynamics where both the wavefunctions for the pure states and operators acting on them arise from the single space/algebra, which exactly includes the WWGM observable algebra. Altogether, putting the emphasis on building our theory out of the underlying relativity symmetry -- the centrally extended Galilean symmetry in the case at hand -- allows one to naturally derive both a kinematical and a dynamical description of a quantum particle, which moreover recovers the corresponding classical picture (understood in terms of the Koopman-von Neumann formalism) in the appropriate (relativity symmetry contraction) limit. Our formulation here is the most natural framework directly connecting all of the relevant mathematical notions and we hope it may help a general physicist better visualize and appreciate the noncommutative-geometric perspective behind quantum physics. It also helps to inspire and illustrate our perspective on looking at quantum mechanics and quantum physics in general in direct connection to the notion of quantum (deformed) relativity symmetries and the corresponding quantum/noncommutative models of spacetime as various levels of approximations all the way down to the Newtonian., Comment: 39 pages, published version

In physics, experiments ultimately inform us as to what constitutes a good theoretical model of any physical concept: physical space should be no exception. The best picture of physical space in Newtonian physics is given by the configuration space of a free particle (or the center of mass of a closed system of particles). This configuration space (as well as phase space), can be constructed as a representation space for the relativity symmetry. From the corresponding quantum symmetry, we illustrate the construction of a quantum configuration space, similar to that of quantum phase space, and recover the classical picture as an approximation through a contraction of the (relativity) symmetry and its representations. The quantum Hilbert space reduces into a sum of one-dimensional representations for the observable algebra, with the only admissible states given by coherent states and position eigenstates for the phase and configuration space pictures, respectively. This analysis, founded firmly on known physics, provides a quantum picture of physical space beyond that of a finite-dimensional manifold, and provides a crucial first link for any theoretical model of quantum spacetime at levels beyond simple quantum mechanics. It also suggests looking at quantum physics from a different perspective., Comment: 19 pages